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Sutherland‐Smith AJ, Carbone V, Schofield LR, Cronin B, Duin EC, Ronimus RS. The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein. FEBS Open Bio 2024; 14:1222-1229. [PMID: 38877345 PMCID: PMC11301259 DOI: 10.1002/2211-5463.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/16/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
Methyl-coenzyme M reductase (MCR) is a multi-subunit (α2β2γ2) enzyme responsible for methane formation via its unique F430 cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.
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Affiliation(s)
| | | | | | - Bryan Cronin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
| | - Evert C. Duin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
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2
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Shi Y, Masic V, Mosaiab T, Rajaratman P, Hartley-Tassell L, Sorbello M, Goulart CC, Vasquez E, Mishra BP, Holt S, Gu W, Kobe B, Ve T. Structural characterization of macro domain-containing Thoeris antiphage defense systems. SCIENCE ADVANCES 2024; 10:eadn3310. [PMID: 38924412 PMCID: PMC11204291 DOI: 10.1126/sciadv.adn3310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD+) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Premraj Rajaratman
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Mitchell Sorbello
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cassia C. Goulart
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Biswa P. Mishra
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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3
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Kabasakal BV, Cotton CAR, Murray JW. Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction. Biochimie 2024; 219:12-20. [PMID: 37952891 DOI: 10.1016/j.biochi.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Malonyl-Coenzyme A Reductase (MCR) in Chloroflexus aurantiacus, a characteristic enzyme of the 3-hydroxypropionate (3-HP) cycle, catalyses the reduction of malonyl-CoA to 3-HP. MCR is a bi-functional enzyme; in the first step, malonyl-CoA is reduced to the free intermediate malonate semialdehyde by the C-terminal region of MCR, and this is further reduced to 3-HP by the N-terminal region of MCR. Here we present the crystal structures of both N-terminal and C-terminal regions of the MCR from C. aurantiacus. A catalytic mechanism is suggested by ligand and substrate bound structures, and structural and kinetic studies of MCR variants. Both MCR structures reveal one catalytic, and one non-catalytic SDR (short chain dehydrogenase/reductase) domain. C-terminal MCR has a lid domain which undergoes a conformational change and controls the reaction. In the proposed mechanism of the C-terminal MCR, the conversion of malonyl-CoA to malonate semialdehyde is based on the reduction of malonyl-CoA by NADPH, followed by the decomposition of the hemithioacetal to produce malonate semialdehyde and coenzyme A. Conserved arginines, Arg734 and Arg773 are proposed to play key roles in the mechanism and conserved Ser719, and Tyr737 are other essential residues forming an oxyanion hole for the substrate intermediates.
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Affiliation(s)
- Burak V Kabasakal
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Turkish Accelerator and Radiation Laboratory, Gölbaşı, 06830, Ankara, Turkiye
| | - Charles A R Cotton
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Cambrium GmbH, Max-Urich-Strasse 3, 13355, Berlin, Germany
| | - James W Murray
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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4
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Rieu P, Beretta VM, Caselli F, Thévénon E, Lucas J, Rizk M, Franchini E, Caporali E, Paleni C, Nanao MH, Kater MM, Dumas R, Zubieta C, Parcy F, Gregis V. The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development. Proc Natl Acad Sci U S A 2024; 121:e2310464121. [PMID: 38412122 DOI: 10.1073/pnas.2310464121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 02/29/2024] Open
Abstract
The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | | | - Francesca Caselli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Emmanuel Thévénon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Mahmoud Rizk
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Chiara Paleni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Max H Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
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Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Dalton Trans 2024; 53:1794-1808. [PMID: 38170898 PMCID: PMC10804444 DOI: 10.1039/d3dt03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.
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Affiliation(s)
- Magali Roger
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Philippe Leone
- CNRS, Aix-Marseille University, Laboratoire d'Ingénierie des Systèmes Macromoléculaires, LISM UMR7255, 13009 Marseille, France
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sam Horrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Frédéric Biaso
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Marie-Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Sciara
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
- Aix Marseille Univ, INRAE, BBF UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Marianne Ilbert
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
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6
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Gao J, Jishage M, Wang Y, Wang R, Chen M, Zhu Z, Zhang J, Diwu Y, Xu C, Liao S, Roeder RG, Tu X. Structural basis for evolutionarily conserved interactions between TFIIS and Paf1C. Int J Biol Macromol 2023; 253:126764. [PMID: 37696373 PMCID: PMC11164251 DOI: 10.1016/j.ijbiomac.2023.126764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
The elongation factor TFIIS interacts with Paf1C complex to facilitate processive transcription by Pol II. We here determined the crystal structure of the trypanosoma TFIIS LW domain in a complex with the LFG motif of Leo1, as well as the structures of apo-form TFIIS LW domains from trypanosoma, yeast and human. We revealed that all three TFIIS LW domains possess a conserved hydrophobic core that mediates their interactions with Leo1. Intriguingly, the structural study revealed that trypanosoma Leo1 binding induces the TFIIS LW domain to undergo a conformational change reflected in the length and orientation of α6 helix that is absent in the yeast and human counterparts. These differences explain the higher binding affinity of the TFIIS LW domain interacting with Leo1 in trypanosoma than in yeast and human, and indicate species-specific variations in the interactions. Importantly, the interactions between the TFIIS LW domain and an LFG motif of Leo1 were found to be critical for TFIIS to anchor the entire Paf1C complex. Thus, in addition to revealing a detailed structural basis for the TFIIS-Paf1C interaction, our studies also shed light on the origin and evolution of the roles of TFIIS and Paf1C complex in regulation of transcription elongation.
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Affiliation(s)
- Jie Gao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China; Department of Ophthalmology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, PR China
| | - Miki Jishage
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yuzhu Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Rui Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China; Department of Anthropotomy and Histoembryology, Medical College, Henan University of Science and Technology, Luoyang, Henan 471023, PR China
| | - Meng Chen
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Jiahai Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Yating Diwu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Shanhui Liao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Xiaoming Tu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China.
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7
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Jespersen M, Wagner T. Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Nat Microbiol 2023:10.1038/s41564-023-01398-8. [PMID: 37277534 DOI: 10.1038/s41564-023-01398-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
Methanothermococcus thermolithotrophicus is the only known methanogen that grows on sulfate as its sole sulfur source, uniquely uniting methanogenesis and sulfate reduction. Here we use physiological, biochemical and structural analyses to provide a snapshot of the complete sulfate reduction pathway of this methanogenic archaeon. We find that later steps in this pathway are catalysed by atypical enzymes. PAPS (3'-phosphoadenosine 5'-phosphosulfate) released by APS kinase is converted into sulfite and 3'-phosphoadenosine 5'-phosphate (PAP) by a PAPS reductase that is similar to the APS reductases of dissimilatory sulfate reduction. A non-canonical PAP phosphatase then hydrolyses PAP. Finally, the F420-dependent sulfite reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that the sulfate reduction pathway is present in several methanogens, the sulfate assimilation pathway in M. thermolithotrophicus is distinct. We propose that this pathway was 'mix-and-matched' through the acquisition of assimilatory and dissimilatory enzymes from other microorganisms and then repurposed to fill a unique metabolic role.
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Affiliation(s)
- Marion Jespersen
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tristan Wagner
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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8
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Shah BS, Ford BA, Varkey D, Mikolajek H, Orr C, Mykhaylyk V, Owens RJ, Paulsen IT. Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter. THE ISME JOURNAL 2023:10.1038/s41396-023-01417-w. [PMID: 37087502 DOI: 10.1038/s41396-023-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Despite being fundamental to multiple biological processes, phosphorus (P) availability in marine environments is often growth-limiting, with generally low surface concentrations. Picocyanobacteria strains encode a putative ABC-type phosphite/phosphate/phosphonate transporter, phnDCE, thought to provide access to an alternative phosphorus pool. This, however, is paradoxical given most picocyanobacterial strains lack known phosphite degradation or carbon-phosphate lyase pathway to utilise alternate phosphorus pools. To understand the function of the PhnDCE transport system and its ecological consequences, we characterised the PhnD1 binding proteins from four distinct marine Synechococcus isolates (CC9311, CC9605, MITS9220, and WH8102). We show the Synechococcus PhnD1 proteins selectively bind phosphorus compounds with a stronger affinity for phosphite than for phosphate or methyl phosphonate. However, based on our comprehensive ligand screening and growth experiments showing Synechococcus strains WH8102 and MITS9220 cannot utilise phosphite or methylphosphonate as a sole phosphorus source, we hypothesise that the picocyanobacterial PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter, and the measured affinity of PhnD1 to phosphite or methyl phosphonate is fortuitous. Our MITS9220_PhnD1 structure explains the comparatively lower affinity of picocyanobacterial PhnD1 for phosphate, resulting from a more limited H-bond network. We propose two possible physiological roles for PhnD1. First, it could function in phospholipid recycling, working together with the predicted phospholipase, TesA, and alkaline phosphatase. Second, by having multiple transporters for P (PhnDCE and Pst), picocyanobacteria could balance the need for rapid transport during transient episodes of higher P availability in the environment, with the need for efficient P utilisation in typical phosphate-deplete conditions.
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Affiliation(s)
- Bhumika S Shah
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
| | - Benjamin A Ford
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Halina Mikolajek
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Christian Orr
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Structural Biology, Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
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9
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Shukla PK, Bissell JE, Kumar S, Pokhrel S, Palani S, Radmall K, Obidi O, Parnell TJ, Brasch J, Shrieve D, Chandrasekharan M. Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. Nucleic Acids Res 2023; 51:2117-2136. [PMID: 36715322 PMCID: PMC10018343 DOI: 10.1093/nar/gkad012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 'backside'. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6-Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6-Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6-Bre1 interaction through a novel interface that is important for their biochemical and biological responses.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sanjit Kumar
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Srijana Pokhrel
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Onyeka Obidi
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julia Brasch
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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10
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Jespersen M, Pierik AJ, Wagner T. Structures of the sulfite detoxifying F 420-dependent enzyme from Methanococcales. Nat Chem Biol 2023; 19:695-702. [PMID: 36658338 DOI: 10.1038/s41589-022-01232-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/22/2022] [Indexed: 01/21/2023]
Abstract
Methanogenic archaea are main actors in the carbon cycle but are sensitive to reactive sulfite. Some methanogens use a sulfite detoxification system that combines an F420H2-oxidase with a sulfite reductase, both of which are proposed precursors of modern enzymes. Here, we present snapshots of this coupled system, named coenzyme F420-dependent sulfite reductase (Group I Fsr), obtained from two marine methanogens. Fsr organizes as a homotetramer, harboring an intertwined six-[4Fe-4S] cluster relay characterized by spectroscopy. The wire, spanning 5.4 nm, electronically connects the flavin to the siroheme center. Despite a structural architecture similar to dissimilatory sulfite reductases, Fsr shows a siroheme coordination and a reaction mechanism identical to assimilatory sulfite reductases. Accordingly, the reaction of Fsr is unidirectional, reducing sulfite or nitrite with F420H2. Our results provide structural insights into this unique fusion, in which a primitive sulfite reductase turns a poison into an elementary block of life.
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Affiliation(s)
| | - Antonio J Pierik
- Biochemistry, Faculty of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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11
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Denkhaus L, Siffert F, Einsle O. An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens. FEMS Microbiol Lett 2023; 370:fnad068. [PMID: 37460131 DOI: 10.1093/femsle/fnad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.
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Affiliation(s)
- Lukas Denkhaus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Fanny Siffert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
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12
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Ru W, Koga T, Wang X, Guo Q, Gearhart MD, Zhao S, Murphy M, Kawakami H, Corcoran D, Zhang J, Zhu Z, Yao X, Kawakami Y, Xu C. Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif. J Biol Chem 2022; 298:102607. [PMID: 36257403 PMCID: PMC9672407 DOI: 10.1016/j.jbc.2022.102607] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
The Spalt-like 4 transcription factor (SALL4) plays an essential role in controlling the pluripotent property of embryonic stem cells via binding to AT-rich regions of genomic DNA, but structural details on this binding interaction have not been fully characterized. Here, we present crystal structures of the zinc finger cluster 4 (ZFC4) domain of SALL4 (SALL4ZFC4) bound with different dsDNAs containing a conserved AT-rich motif. In the structures, two zinc fingers of SALL4ZFC4 recognize an AATA tetranucleotide. We also solved the DNA-bound structures of SALL3ZFC4 and SALL4ZFC1. These structures illuminate a common preference for the AATA tetranucleotide shared by ZFC4 of SALL1, SALL3, and SALL4. Furthermore, our cell biology experiments demonstrate that the DNA-binding activity is essential for SALL4 function as DNA-binding defective mutants of mouse Sall4 failed to repress aberrant gene expression in Sall4-/- mESCs. Thus, these analyses provide new insights into the mechanisms of action underlying SALL family proteins in controlling cell fate via preferential targeting to AT-rich sites within genomic DNA during cell differentiation.
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Affiliation(s)
- Wenwen Ru
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Xiaoyang Wang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Qiong Guo
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Shidong Zhao
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Mark Murphy
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jiahai Zhang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Zhongliang Zhu
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA; Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Chao Xu
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China.
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13
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d'Amico EA, Ud Din Ahmad M, Cmentowski V, Girbig M, Müller F, Wohlgemuth S, Brockmeyer A, Maffini S, Janning P, Vetter IR, Carter AP, Perrakis A, Musacchio A. Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin. J Cell Biol 2022; 221:213466. [PMID: 36107127 PMCID: PMC9481740 DOI: 10.1083/jcb.202206131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Cytoplasmic Dynein 1, or Dynein, is a microtubule minus end-directed motor. Dynein motility requires Dynactin and a family of activating adaptors that stabilize the Dynein-Dynactin complex and promote regulated interactions with cargo in space and time. How activating adaptors limit Dynein activation to specialized subcellular locales is unclear. Here, we reveal that Spindly, a mitotic Dynein adaptor at the kinetochore corona, exists natively in a closed conformation that occludes binding of Dynein-Dynactin to its CC1 box and Spindly motif. A structure-based analysis identified various mutations promoting an open conformation of Spindly that binds Dynein-Dynactin. A region of Spindly downstream from the Spindly motif and not required for cargo binding faces the CC1 box and stabilizes the intramolecular closed conformation. This region is also required for robust kinetochore localization of Spindly, suggesting that kinetochores promote Spindly activation to recruit Dynein. Thus, our work illustrates how specific Dynein activation at a defined cellular locale may require multiple factors.
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Affiliation(s)
- Ennio A d'Amico
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Misbha Ud Din Ahmad
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Verena Cmentowski
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | | | - Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andreas Brockmeyer
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Anastassis Perrakis
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
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14
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Ahlqvist J, Linares-Pastén JA, Jasilionis A, Welin M, Håkansson M, Svensson LA, Wang L, Watzlawick H, Ævarsson A, Friðjónsson ÓH, Hreggviðsson GÓ, Ketelsen Striberny B, Glomsaker E, Lanes O, Al-Karadaghi S, Nordberg Karlsson E. Crystal structure of DNA polymerase I from Thermus phage G20c. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:1384-1398. [DOI: 10.1107/s2059798322009895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3′–5′ exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5′–3′ exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3′–5′ exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.
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15
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The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3. Commun Biol 2022; 5:954. [PMID: 36097056 PMCID: PMC9468336 DOI: 10.1038/s42003-022-03869-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
Abstract
Choanoflagellates are primitive protozoa used as models for animal evolution. They express a large variety of multi-domain proteins contributing to adhesion and cell communication, thereby providing a rich repertoire of molecules for biotechnology. Adhesion often involves proteins adopting a β-trefoil fold with carbohydrate-binding properties therefore classified as lectins. Sequence database screening with a dedicated method resulted in TrefLec, a database of 44714 β-trefoil candidate lectins across 4497 species. TrefLec was searched for original domain combinations, which led to single out SaroL-1 in the choanoflagellate Salpingoeca rosetta, that contains both β-trefoil and aerolysin-like pore-forming domains. Recombinant SaroL-1 is shown to bind galactose and derivatives, with a stronger affinity for cancer-related α-galactosylated epitopes such as the glycosphingolipid Gb3, when embedded in giant unilamellar vesicles or cell membranes. Crystal structures of complexes with Gb3 trisaccharide and GalNAc provided the basis for building a model of the oligomeric pore. Finally, recognition of the αGal epitope on glycolipids required for hemolysis of rabbit erythrocytes suggests that toxicity on cancer cells is achieved through carbohydrate-dependent pore-formation. A curated lectin database, structural characterization, and in vitro assays show that choanoflagellate lectin SaroL-1 binds to cancer-related α-galactosylated epitopes and can be toxic to cancer cells through a carbohydrate-dependent pore-formation mechanism.
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16
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Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum. mBio 2022; 13:e0147622. [PMID: 36069444 PMCID: PMC9601137 DOI: 10.1128/mbio.01476-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sugar uptake is of great significance in industrially relevant microorganisms. Clostridium thermocellum has extensive potential in lignocellulose biorefineries as an environmentally prominent, thermophilic, cellulolytic bacterium. The bacterium employs five putative ATP-binding cassette transporters which purportedly take up cellulose hydrolysates. Here, we first applied combined genetic manipulations and biophysical titration experiments to decipher the key glucose and cellodextrin transporters. In vivo gene inactivation of each transporter and in vitro calorimetric and nuclear magnetic resonance (NMR) titration of each putative sugar-binding protein with various saccharides supported the conclusion that only transporters A and B play the roles of glucose and cellodextrin transport, respectively. To gain insight into the structural mechanism of the transporter specificities, 11 crystal structures, both alone and in complex with appropriate saccharides, were solved for all 5 putative sugar-binding proteins, thus providing detailed specific interactions between the proteins and the corresponding saccharides. Considering the importance of transporter B as the major cellodextrin transporter, we further identified its cryptic, hitherto unknown ATPase-encoding gene as clo1313_2554, which is located outside the transporter B gene cluster. The crystal structure of the ATPase was solved, showing that it represents a typical nucleotide-binding domain of the ATP-binding cassette (ABC) transporter. Moreover, we determined that the inducing effect of cellobiose (G2) and cellulose on cellulosome production could be eliminated by deletion of transporter B genes, suggesting the coupling of sugar transport and regulation of cellulosome components. This study provides key basic information on the sugar uptake mechanism of C. thermocellum and will promote rational engineering of the bacterium for industrial application.
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17
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Kuang Z, Ke J, Hong J, Zhu Z, Niu L. Structural assembly of the nucleic-acid-binding Thp3-Csn12-Sem1 complex functioning in mRNA splicing. Nucleic Acids Res 2022; 50:8882-8897. [PMID: 35904806 PMCID: PMC9410885 DOI: 10.1093/nar/gkac634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/26/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
PCI domain proteins play important roles in post-transcriptional gene regulation. In the TREX-2 complex, PCI domain-containing Sac3 and Thp1 proteins and accessory Sem1 protein form a ternary complex required for mRNA nuclear export. In contrast, structurally related Thp3–Csn12–Sem1 complex mediates pre-mRNA splicing. In this study, we determined the structure of yeast Thp3186–470–Csn12–Sem1 ternary complex at 2.9 Å resolution. Both Thp3 and Csn12 structures have a typical PCI structural fold, characterized by a stack of α-helices capped by a C-terminal winged-helix (WH) domain. The overall structure of Thp3186–470–Csn12–Sem1 complex has an inverted V-shape with Thp3 and Csn12 forming the two sides. A fishhook-shaped Sem1 makes extensive contacts on Csn12 to stabilize its conformation. The overall structure of Thp3186–470–Csn12–Sem1 complex resembles the previously reported Sac3–Thp1–Sem1 complex, but also has significant structural differences. The C-terminal WH domains of Thp3 and Csn12 form a continuous surface to bind different forms of nucleic acids with micromolar affinity. Mutation of the basic residues in the WH domains of Thp3 and Csn12 affects nucleic acid binding in vitro and mRNA splicing in vivo. The Thp3–Csn12–Sem1 structure provides a foundation for further exploring the structural elements required for its specific recruitment to spliceosome for pre-mRNA splicing.
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Affiliation(s)
- Zhiling Kuang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiyuan Ke
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Northwest corner of Susong Rd & Guanhai Rd, Hefei, Anhui 230601, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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18
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Landskron L, Bak J, Adamopoulos A, Kaplani K, Moraiti M, van den Hengel LG, Song JY, Bleijerveld OB, Nieuwenhuis J, Heidebrecht T, Henneman L, Moutin MJ, Barisic M, Taraviras S, Perrakis A, Brummelkamp TR. Posttranslational modification of microtubules by the MATCAP detyrosinase. Science 2022; 376:eabn6020. [PMID: 35482892 DOI: 10.1126/science.abn6020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small vasohibin-binding protein (SVBP) complex underlies much, but not all, detyrosination. We used haploid genetic screens to identify an unannotated protein, microtubule associated tyrosine carboxypeptidase (MATCAP), as a remaining detyrosinating enzyme. X-ray crystallography and cryo-electron microscopy structures established MATCAP's cleaving mechanism, substrate specificity, and microtubule recognition. Paradoxically, whereas abrogation of tyrosine religation is lethal in mice, codeletion of MATCAP and SVBP is not. Although viable, defective detyrosination caused microcephaly, associated with proliferative defects during neurogenesis, and abnormal behavior. Thus, MATCAP is a missing component of the detyrosination-tyrosination cycle, revealing the importance of this modification in brain formation.
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Affiliation(s)
- Lisa Landskron
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Jitske Bak
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Athanassios Adamopoulos
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Konstantina Kaplani
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Maria Moraiti
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Lisa G van den Hengel
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Ji-Ying Song
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Joppe Nieuwenhuis
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Linda Henneman
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Marie-Jo Moutin
- Université Grenoble Alpes, INSERM, U1216, CNRS, Grenoble Institut Neurosciences, 38000 Grenoble, France
| | - Marin Barisic
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center (DCRC), 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
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19
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Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. Commun Biol 2022; 5:312. [PMID: 35383272 PMCID: PMC8983713 DOI: 10.1038/s42003-022-03269-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Obtaining the high-resolution structures of proteins and their complexes is a crucial aspect of understanding the mechanisms of life. Experimental structure determination methods are time-consuming, expensive and cannot keep pace with the growing number of protein sequences available through genomic DNA sequencing. Thus, the ability to accurately predict the structure of proteins from their sequence is a holy grail of structural and computational biology that would remove a bottleneck in our efforts to understand as well as rationally engineer living systems. Recent advances in protein structure prediction, in particular the breakthrough with the AI-based tool AlphaFold2 (AF2), hold promise for achieving this goal, but the practical utility of AF2 remains to be explored. Focusing on proteins with essential roles in centrosome and centriole biogenesis, we demonstrate the quality and usability of the AF2 prediction models and we show that they can provide important insights into the modular organization of two key players in this process, CEP192 and CEP44. Furthermore, we used the AF2 algorithm to elucidate and then experimentally validate previously unknown prime features in the structure of TTBK2 bound to CEP164, as well as the Chibby1-FAM92A complex for which no structural information was available to date. These findings have important implications in understanding the regulation and function of these complexes. Finally, we also discuss some practical limitations of AF2 and anticipate the implications for future research approaches in the centriole/centrosome field. Using experimental data, the authors assess the quality and discuss the limitations of AlphaFold2 predictions of protein structures and protein-protein interactions essential for centrosome and centriole biogenesis.
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20
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Cornish KAS, Lange J, Aevarsson A, Pohl E. CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins. J Biol Chem 2022; 298:101919. [PMID: 35405098 PMCID: PMC9108980 DOI: 10.1016/j.jbc.2022.101919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
The Candidate Phyla Radiation is a recently uncovered and vast expansion of the bacterial domain of life, made up of largely uncharacterized phyla that lack isolated representatives. This unexplored territory of genetic diversity presents an abundance of novel proteins with potential applications in the life-science sectors. Here, we present the structural and functional elucidation of CPR-C4, a hypothetical protein from the genome of a thermophilic Candidate Phyla Radiation organism, identified through metagenomic sequencing. Our analyses revealed that CPR-C4 is a member of a family of highly conserved proteins within the Candidate Phyla Radiation. The function of CPR-C4 as a cysteine protease was predicted through remote structural similarity to the Homo sapiens vasohibins and subsequently confirmed experimentally with fluorescence-based activity assays. Furthermore, detailed structural and sequence alignment analysis enabled identification of a noncanonical cysteine-histidine-leucine(carbonyl) catalytic triad. The unexpected structural and functional similarities between CPR-C4 and the human vasohibins suggest an evolutionary relationship undetectable at the sequence level alone.
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Affiliation(s)
- Katy A S Cornish
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, County Durham, United Kingdom
| | | | | | - Ehmke Pohl
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, County Durham, United Kingdom; Department of Biosciences, Durham University, Upper Mountjoy, Durham, County Durham, United Kingdom.
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21
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Yu S, Sui Y, Wang J, Li Y, Li H, Cao Y, Chen L, Jiang L, Yuan C, Huang M. Crystal structure and cellular functions of uPAR dimer. Nat Commun 2022; 13:1665. [PMID: 35351875 PMCID: PMC8964761 DOI: 10.1038/s41467-022-29344-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/25/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractReceptor dimerization of urokinase-type plasminogen activator receptor (uPAR) was previously identified at protein level and on cell surface. Recently, a dimeric form of mouse uPAR isoform 2 was proposed to induce kidney disease. Here, we report the crystal structure of human uPAR dimer at 2.96 Å. The structure reveals enormous conformational changes of the dimer compared to the monomeric structure: D1 of uPAR opens up into a large expanded ring that captures a β-hairpin loop of a neighboring uPAR to form an expanded β-sheet, leading to an elongated, highly intertwined dimeric uPAR. Based on the structure, we identify E49P as a mutation promoting dimer formation. The mutation increases receptor binding to the amino terminal fragment of its primary ligand uPA, induces the receptor to distribute to the basal membrane, promotes cell proliferation, and alters cell morphology via β1 integrin signaling. These results reveal the structural basis for uPAR dimerization, its effect on cellular functions, and provide a basis to further study this multifunctional receptor.
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22
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Nanao M, Basu S, Zander U, Giraud T, Surr J, Guijarro M, Lentini M, Felisaz F, Sinoir J, Morawe C, Vivo A, Beteva A, Oscarsson M, Caserotto H, Dobias F, Flot D, Nurizzo D, Gigmes J, Foos N, Siebrecht R, Roth T, Theveneau P, Svensson O, Papp G, Lavault B, Cipriani F, Barrett R, Clavel C, Leonard G. ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:581-590. [PMID: 35254323 PMCID: PMC8900849 DOI: 10.1107/s1600577522000984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/28/2022] [Indexed: 05/30/2023]
Abstract
ID23-2 is a fixed-energy (14.2 keV) microfocus beamline at the European Synchrotron Radiation Facility (ESRF) dedicated to macromolecular crystallography. The optics and sample environment have recently been redesigned and rebuilt to take full advantage of the upgrade of the ESRF to the fourth generation Extremely Brilliant Source (ESRF-EBS). The upgraded beamline now makes use of two sets of compound refractive lenses and multilayer mirrors to obtain a highly intense (>1013 photons s-1) focused microbeam (minimum size 1.5 µm × 3 µm full width at half-maximum). The sample environment now includes a FLEX-HCD sample changer/storage system, as well as a state-of-the-art MD3Up high-precision multi-axis diffractometer. Automatic data reduction and analysis are also provided for more advanced protocols such as synchrotron serial crystallographic experiments.
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Affiliation(s)
- Max Nanao
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christian Morawe
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Amparo Vivo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Jonathan Gigmes
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Nicolas Foos
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Thomas Roth
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gergely Papp
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Florent Cipriani
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Carole Clavel
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gordon Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
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23
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C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat Commun 2021; 12:6294. [PMID: 34728636 PMCID: PMC8563793 DOI: 10.1038/s41467-021-26585-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/12/2021] [Indexed: 01/14/2023] Open
Abstract
C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.
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24
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Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun 2021; 12:6078. [PMID: 34667177 PMCID: PMC8526623 DOI: 10.1038/s41467-021-26360-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Melania Bruno
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tanja Kaufmann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ursula E Schoeberl
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin G Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Carmen Ebenwaldner
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Marek Sebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Etienne Beltzung
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gen Lin
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Martin Leeb
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Carrie Bernecky
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, Klosterneuburg, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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25
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FAD-dependent C-glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis. Proc Natl Acad Sci U S A 2021; 118:2106580118. [PMID: 34583991 DOI: 10.1073/pnas.2106580118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
C-glycosides have a unique structure, in which an anomeric carbon of a sugar is directly bonded to the carbon of an aglycone skeleton. One of the natural C-glycosides, carminic acid, is utilized by the food, cosmetic, and pharmaceutical industries, for a total of more than 200 tons/y worldwide. However, a metabolic pathway of carminic acid has never been identified. In this study, we isolated the previously unknown carminic acid-catabolizing microorganism and discovered a flavoenzyme "C-glycoside 3-oxidase" named CarA that catalyzes oxidation of the sugar moiety of carminic acid. A Basic Local Alignment Search Tool (BLAST) search demonstrated that CarA homologs were distributed in soil microorganisms but not intestinal ones. In addition to CarA, two CarA homologs were cloned and heterologously expressed, and their biochemical properties were determined. Furthermore, a crystal structure of one homolog was determined. Together with the biochemical analysis, the crystal structure and a mutagenesis analysis of CarA revealed the mechanisms underlying their substrate specificity and catalytic reaction. Our study suggests that CarA and its homologs play a crucial role in the metabolism of C-glycosides in nature.
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26
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Wang X, Zeng C, Liao S, Zhu Z, Zhang J, Tu X, Yao X, Feng X, Guang S, Xu C. Molecular basis for PICS-mediated piRNA biogenesis and cell division. Nat Commun 2021; 12:5595. [PMID: 34552083 PMCID: PMC8458385 DOI: 10.1038/s41467-021-25896-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/02/2021] [Indexed: 11/12/2022] Open
Abstract
By incorporating two mutually exclusive factors, PID-1 and TOST-1, C. elegans PICS complex plays important roles in piRNA biogenesis, chromosome segregation and cell division. We firstly map the interaction network between PICS subunits, then uncover the mechanisms underlying the interactions between PICS subunits by solving several complex structures, including those of TOFU-6/PICS-1, ERH-2/PICS-1, and ERH-2/TOST-1. Our biochemical experiment also demonstrates that PICS exists as an octamer consisting of two copies of each subunit. Combining structural analyses with mutagenesis experiments, we identify interfacial residues of PICS subunits that are critical for maintaining intact PICS complex in vitro. Furthermore, using genetics, cell biology and imaging experiments, we find that those mutants impairing the in vitro interaction network within PICS, also lead to dysfunction of PICS in vivo, including mislocalization of PICS, and reduced levels of piRNAs or aberrant chromosome segregation and cell division. Therefore, our work provides structural insights into understanding the PICS-mediated piRNA biogenesis and cell division. C. elegans piRNA biogenesis and chromosome segregation (PICS) complex is composed of TOFU-6, PICS-1, ERH-2, and two mutually exclusive factors PID-1 and TOST-1. By employing biochemical, structural, and cellular biology methods, the authors show that the PICS complex is an octamer consisting of two copies of each subunit, and functions in piRNA biogenesis and mitosis.
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Affiliation(s)
- Xiaoyang Wang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Chenming Zeng
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Shanhui Liao
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Zhongliang Zhu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Xiaoming Tu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Xuebiao Yao
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China
| | - Xuezhu Feng
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China.
| | - Shouhong Guang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China. .,Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China.
| | - Chao Xu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China.
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27
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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28
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You C, Li F, Zhang X, Ma L, Zhang YZ, Zhang W, Li S. Structural basis for substrate specificity of the peroxisomal acyl-CoA hydrolase MpaH' involved in mycophenolic acid biosynthesis. FEBS J 2021; 288:5768-5780. [PMID: 33843134 DOI: 10.1111/febs.15874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 11/30/2022]
Abstract
Mycophenolic acid (MPA) is a fungal natural product and first-line immunosuppressive drug for organ transplantations and autoimmune diseases. In the compartmentalized biosynthesis of MPA, the acyl-coenzyme A (CoA) hydrolase MpaH' located in peroxisomes catalyzes the highly specific hydrolysis of MPA-CoA to produce the final product MPA. The strict substrate specificity of MpaH' not only averts undesired hydrolysis of various cellular acyl-CoAs, but also prevents MPA-CoA from further peroxisomal β-oxidation catabolism. To elucidate the structural basis for this important property, in this study, we solve the crystal structures of the substrate-free form of MpaH' and the MpaH'S139A mutant in complex with the product MPA. The MpaH' structure reveals a canonical α/β-hydrolase fold with an unusually large cap domain and a rare location of the acidic residue D163 of catalytic triad after strand β6. MpaH' also forms an atypical dimer with the unique C-terminal helices α13 and α14 arming the cap domain of the other protomer and indirectly participating in the substrate binding. With these characteristics, we propose that MpaH' and its homologs form a new subfamily of α/β hydrolase fold protein. The crystal structure of MpaH'S139A /MPA complex and the modeled structure of MpaH'/MPA-CoA, together with the structure-guided mutagenesis analysis and isothermal titration calorimetry (ITC) measurements, provide important mechanistic insights into the high substrate specificity of MpaH'.
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Affiliation(s)
- Cai You
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fengwei Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China
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29
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Chen X, Liao S, Makaros Y, Guo Q, Zhu Z, Krizelman R, Dahan K, Tu X, Yao X, Koren I, Xu C. Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase. Nat Chem Biol 2021; 17:254-262. [PMID: 33398168 DOI: 10.1038/s41589-020-00704-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
Degrons are elements within protein substrates that mediate the interaction with specific degradation machineries to control proteolysis. Recently, a few classes of C-terminal degrons (C-degrons) that are recognized by dedicated cullin-RING ligases (CRLs) have been identified. Specifically, CRL2 using the related substrate adapters FEM1A/B/C was found to recognize C degrons ending with arginine (Arg/C-degron). Here, we uncover the molecular mechanism of Arg/C-degron recognition by solving a subset of structures of FEM1 proteins in complex with Arg/C-degron-bearing substrates. Our structural research, complemented by binding assays and global protein stability (GPS) analyses, demonstrates that FEM1A/C and FEM1B selectively target distinct classes of Arg/C-degrons. Overall, our study not only sheds light on the molecular mechanism underlying Arg/C-degron recognition for precise control of substrate turnover, but also provides valuable information for development of chemical probes for selectively regulating proteostasis.
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Affiliation(s)
- Xinyan Chen
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shanhui Liao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Qiong Guo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Rina Krizelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Karin Dahan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Xiaoming Tu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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Mehr A, Henneberg F, Chari A, Görlich D, Huyton T. The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography. Acta Crystallogr D Struct Biol 2020; 76:1222-1232. [PMID: 33263328 PMCID: PMC7709198 DOI: 10.1107/s2059798320013741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
The growth of diffraction-quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high-affinity copper(II)-binding tripeptide GHK was fused to the N-terminus of a GFP variant and an MBP-FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square-pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S-atom positions could also be located in log-likelihood-gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR-SAD phasing.
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Affiliation(s)
- Alexander Mehr
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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31
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Molecular basis for cysteine oxidation by plant cysteine oxidases from Arabidopsis thaliana. J Struct Biol 2020; 213:107663. [PMID: 33207269 DOI: 10.1016/j.jsb.2020.107663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Plant Cysteine Oxidases (PCOs) play important roles in controlling the stability of Group VII ethylene response factors (ERF-VIIs) via Arg/N-degron pathway through catalyzing the oxidation of their N-Cys for subsequent Arginyl-tRNA--protein transferase 1 (ATE1) mediated arginine installation. Here we presented the crystal structures of PCO2, PCO4, and PCO5 from Arabidopsis thaliana (AtPCOs) and examined their in vitro activity by Mass spectrometry (MS). On the basis of Tris-bound AtPCO2, we modelled the structure of Cys-bound AtPCO2 and identified key AtPCO2 residues involved in N-Cys recognition and oxidation. Alanine substitution of potential N-Cys interaction residues impaired the activity of AtPCO5 remarkably. The structural research, complemented by mutagenesis and MS experiments, not only uncovers the substrate recognition and catalytic mode by AtPCOs, but also sheds light on the future design of potent inhibitors for plant cysteine oxidases.
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32
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McGregor NGS, Turkenburg JP, Mørkeberg Krogh KBR, Nielsen JE, Artola M, Stubbs KA, Overkleeft HS, Davies GJ. Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Acta Crystallogr D Struct Biol 2020; 76:1124-1133. [PMID: 33135683 PMCID: PMC7604909 DOI: 10.1107/s205979832001253x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 03/17/2023] Open
Abstract
α-L-Arabinofuranosidases from glycoside hydrolase family 51 use a stereochemically retaining hydrolytic mechanism to liberate nonreducing terminal α-L-arabinofuranose residues from plant polysaccharides such as arabinoxylan and arabinan. To date, more than ten fungal GH51 α-L-arabinofuranosidases have been functionally characterized, yet no structure of a fungal GH51 enzyme has been solved. In contrast, seven bacterial GH51 enzyme structures, with low sequence similarity to the fungal GH51 enzymes, have been determined. Here, the crystallization and structural characterization of MgGH51, an industrially relevant GH51 α-L-arabinofuranosidase cloned from Meripilus giganteus, are reported. Three crystal forms were grown in different crystallization conditions. The unliganded structure was solved using sulfur SAD data collected from a single crystal using the I23 in vacuo diffraction beamline at Diamond Light Source. Crystal soaks with arabinose, 1,4-dideoxy-1,4-imino-L-arabinitol and two cyclophellitol-derived arabinose mimics reveal a conserved catalytic site and conformational itinerary between fungal and bacterial GH51 α-L-arabinofuranosidases.
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Affiliation(s)
- Nicholas G. S. McGregor
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | - Jens Erik Nielsen
- Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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Bond PS, Wilson KS, Cowtan KD. Predicting protein model correctness in Coot using machine learning. Acta Crystallogr D Struct Biol 2020; 76:713-723. [PMID: 32744253 PMCID: PMC7397494 DOI: 10.1107/s2059798320009080] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/02/2020] [Indexed: 11/11/2022] Open
Abstract
Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that is produced by combining multiple sources of information using a neural network. The residues in 639 automatically built models were marked as correct or incorrect by comparing them with the coordinates deposited in the PDB. A number of features were also calculated for each residue using Coot, including map-to-model correlation, density values, B factors, clashes, Ramachandran scores, rotamer scores and resolution. Two neural networks were created using these features as inputs: one to predict the correctness of main-chain atoms and the other for side chains. The 639 structures were split into 511 that were used to train the neural networks and 128 that were used to test performance. The predicted correctness scores could correctly categorize 92.3% of the main-chain atoms and 87.6% of the side chains. A Coot ML Correctness script was written to display the scores in a graphical user interface as well as for the automatic pruning of chains, residues and side chains with low scores. The automatic pruning function was added to the CCP4i2 Buccaneer automated model-building pipeline, leading to significant improvements, especially for high-resolution structures.
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Affiliation(s)
- Paul S. Bond
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Keith S. Wilson
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Kevin D. Cowtan
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol 2020; 16:415-422. [DOI: 10.1038/s41589-019-0461-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/20/2019] [Indexed: 11/09/2022]
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Whelan F, Lafita A, Griffiths SC, Cooper REM, Whittingham JL, Turkenburg JP, Manfield IW, St. John AN, Paci E, Bateman A, Potts JR. Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection. Proc Natl Acad Sci U S A 2019; 116:26540-26548. [PMID: 31818940 PMCID: PMC6936399 DOI: 10.1073/pnas.1911776116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus groups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the β-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin β-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain.
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Affiliation(s)
- Fiona Whelan
- Department of Biology, The University of York, YO10 5DD York, United Kingdom
| | - Aleix Lafita
- European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom
| | - Samuel C. Griffiths
- Department of Biology, The University of York, YO10 5DD York, United Kingdom
| | | | - Jean L. Whittingham
- York Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Iain W. Manfield
- Astbury Centre for Structural Molecular Biology, The University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Alexander N. St. John
- Astbury Centre for Structural Molecular Biology, The University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, The University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom
| | - Jennifer R. Potts
- Department of Biology, The University of York, YO10 5DD York, United Kingdom
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Structure and regulation of ZCCHC4 in m 6A-methylation of 28S rRNA. Nat Commun 2019; 10:5042. [PMID: 31695039 PMCID: PMC6834594 DOI: 10.1038/s41467-019-12923-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) modification provides an important epitranscriptomic mechanism that critically regulates RNA metabolism and function. However, how m6A writers attain substrate specificities remains unclear. We report the 3.1 Å-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m6A methyltransferase, bound to S-adenosyl-L-homocysteine. The methyltransferase (MTase) domain of ZCCHC4 is packed against N-terminal GRF-type and C2H2 zinc finger domains and a C-terminal CCHC domain, creating an integrated RNA-binding surface. Strikingly, the MTase domain adopts an autoinhibitory conformation, with a self-occluded catalytic site and a fully-closed cofactor pocket. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity. Overall, this study unveils unique structural and enzymatic characteristics of ZCCHC4, distinctive from what was seen with the METTL family of m6A writers, providing the mechanistic basis for ZCCHC4 modulation of m6A RNA methylation. The N6-methyladenosine (m6A) RNA modification is an evolutionarily conserved epitranscriptomic mechanism that impacts several cellular processes. Here the authors present a structure-function analysis of the ZCCHC4, 28S RNA-specific m6A methyltransferase, shedding light on its regulation and mechanisms that ensure substrate specificity.
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Freitag-Pohl S, Jasilionis A, Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E. Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol 2019; 75:1028-1039. [PMID: 31692476 PMCID: PMC6834076 DOI: 10.1107/s2059798319013330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022] Open
Abstract
As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.
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Affiliation(s)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Rebeka Kovačič
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Hildegard Watzlawick
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lei Wang
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Magdalena Płotka
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Anna Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | | | | | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, England
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Bule P, Chuzel L, Blagova E, Wu L, Gray MA, Henrissat B, Rapp E, Bertozzi CR, Taron CH, Davies GJ. Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Nat Commun 2019; 10:4816. [PMID: 31645552 PMCID: PMC6811678 DOI: 10.1038/s41467-019-12684-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Sialic acids are a family of related sugars that play essential roles in many biological events intimately linked to cellular recognition in both health and disease. Sialidases are therefore orchestrators of cellular biology and important therapeutic targets for viral infection. Here, we sought to define if uncharacterized sialidases would provide distinct paradigms in sialic acid biochemistry. We show that a recently discovered sialidase family, whose first member EnvSia156 was isolated from hot spring metagenomes, defines an unusual structural fold and active centre constellation, not previously described in sialidases. Consistent with an inverting mechanism, EnvSia156 reveals a His/Asp active center in which the His acts as a Brønsted acid and Asp as a Brønsted base in a single-displacement mechanism. A predominantly hydrophobic aglycone site facilitates accommodation of a variety of 2-linked sialosides; a versatility that offers the potential for glycan hydrolysis across a range of biological and technological platforms.
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Affiliation(s)
- Pedro Bule
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Léa Chuzel
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Elena Blagova
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Liang Wu
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Melissa A Gray
- Department of Chemistry, Stanford University, Stanford, CA, 94305-4404, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
- glyXera GmbH, Leipziger Strasse 44-ZENIT, Magdeburg, Germany
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, 94305-4404, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305-4404, USA
| | | | - Gideon J Davies
- Department of Chemistry, University of York, York, YO10 5DD, UK.
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Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. Nat Commun 2019; 10:3868. [PMID: 31455765 PMCID: PMC6711958 DOI: 10.1038/s41467-019-11740-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) underlie the biosynthesis of many natural products that have important medicinal utility. Protection of the NRPS peptide products from proteolysis is critical to these pathways and is often achieved by structural modification, principally the introduction of d-amino acid residues into the elongating peptide. These amino acids are generally formed in situ from their l-stereoisomers by epimerization domains or dual-function condensation/epimerization domains. In singular contrast, the thioesterase domain of nocardicin biosynthesis mediates both the effectively complete l- to d-epimerization of its C-terminal amino acid residue (≥100:1) and hydrolytic product release. We report herein high-resolution crystal structures of the nocardicin thioesterase domain in ligand-free form and reacted with a structurally precise fluorophosphonate substrate mimic that identify the complete peptide binding pocket to accommodate both stereoisomers. These structures combined with additional functional studies provide detailed mechanistic insight into this unique dual-function NRPS domain. NocTE is a nonribosomal peptide synthetase thioesterase that completes the biosynthesis of pro-nocardicin G, the precursor for nocardicin β-lactam antibiotics. Here the authors provide mechanistic insights into NocTE by determining its crystal structures in the ligand-free form and covalently linked to a fluorophosphonate substrate mimic.
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40
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Liao S, Rajendraprasad G, Wang N, Eibes S, Gao J, Yu H, Wu G, Tu X, Huang H, Barisic M, Xu C. Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. Cell Res 2019; 29:533-547. [PMID: 31171830 DOI: 10.1038/s41422-019-0187-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/15/2019] [Indexed: 12/31/2022] Open
Abstract
α-Tubulin detyrosination, largely catalyzed by vasohibins, is involved in many microtubule (MT)-related cellular events. In this study, we identified a core heterodimeric complex of human small vasohibin-binding protein (SVBP) and vasohibin 1 (VASH1) (hereafter denoted as SVBP-VASH1) that catalyzes the detyrosination of a peptide derived from C-terminus of α-tubulin. We further solved the crystal structures of the SVBP-VASH1 heterodimer alone and in complex with either an inhibitor or a mutant substrate peptide. Our structural research, complemented by biochemical and mutagenesis experiments, resulted in identification of the key residues for VASH1 binding to SVBP and α-tubulin substrate. Our in vivo experiments reveal that MT detyrosination in general, as well as the interactions between SVBP, VASH1, and α-tubulin, are critical for spindle function and accurate chromosome segregation during mitosis. Furthermore, we found that the phenotypes caused by the depletion of vasohibins were largely rescued upon co-depletion of kinesin13/MCAK, suggesting the coordination between the MT depolymerase and MT detyrosination during mitosis. Thus our work not only provides structural insights into the molecular mechanism of α-tubulin detyrosination catalyzed by SVBP-bound vasohibins, but also uncovers the key role of vasohibins-mediated MT detyrosination in spindle morphology and chromosome segregation during mitosis.
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Affiliation(s)
- Shanhui Liao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Girish Rajendraprasad
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Na Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Susana Eibes
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Jun Gao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Huijuan Yu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Gao Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hongda Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.
| | - Marin Barisic
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark. .,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Chao Xu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.
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Dorsey BW, Huang L, Mondragón A. Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM. Nucleic Acids Res 2019; 47:3765-3783. [PMID: 30759237 PMCID: PMC6468305 DOI: 10.1093/nar/gkz079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and types. Class 1 CRISPR-Cas systems form multi-protein effector complexes that includes a guide RNA (crRNA) used to identify the target for destruction. Here we present crystal structures of Staphylococcus epidermidis Type III-A CRISPR subunits Csm2 and Csm3 and a 5.2 Å resolution single-particle cryo-electron microscopy (cryo-EM) reconstruction of an in vivo assembled effector subcomplex including the crRNA. The structures help to clarify the quaternary architecture of Type III-A effector complexes, and provide details on crRNA binding, target RNA binding and cleavage, and intermolecular interactions essential for effector complex assembly. The structures allow a better understanding of the organization of Type III-A CRISPR effector complexes as well as highlighting the overall similarities and differences with other Class 1 effector complexes.
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Affiliation(s)
- Bryan W Dorsey
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Lei Huang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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42
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Schopf FH, Huber EM, Dodt C, Lopez A, Biebl MM, Rutz DA, Mühlhofer M, Richter G, Madl T, Sattler M, Groll M, Buchner J. The Co-chaperone Cns1 and the Recruiter Protein Hgh1 Link Hsp90 to Translation Elongation via Chaperoning Elongation Factor 2. Mol Cell 2019; 74:73-87.e8. [PMID: 30876805 DOI: 10.1016/j.molcel.2019.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 12/31/2022]
Abstract
The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast, but its structure and function remained unknown. Here, we report the X-ray structure of the Cns1 fold and NMR studies on the partly disordered, essential segment of the protein. We demonstrate that Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90. The in vivo folding and solubility of eEF2 depend on the presence of these proteins. Chaperoning of eEF2 by Cns1 is essential for yeast viability and requires a defined subset of the Hsp90 machinery as well as the identified eEF2 recruiting factor Hgh1.
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Affiliation(s)
- Florian H Schopf
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Eva M Huber
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Christopher Dodt
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Abraham Lopez
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Maximilian M Biebl
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Daniel A Rutz
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Moritz Mühlhofer
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Gesa Richter
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Michael Sattler
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Groll
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany.
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43
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Cuppari A, Körschgen H, Fahrenkamp D, Schmitz C, Guevara T, Karmilin K, Kuske M, Olf M, Dietzel E, Yiallouros I, de Sanctis D, Goulas T, Weiskirchen R, Jahnen-Dechent W, Floehr J, Stoecker W, Jovine L, Gomis-Rüth FX. Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition. IUCRJ 2019; 6:317-330. [PMID: 30867929 PMCID: PMC6400186 DOI: 10.1107/s2052252519001568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWVXGP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWVXGP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.
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Affiliation(s)
- Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Konstantin Karmilin
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Mario Olf
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Eileen Dietzel
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Walter Stoecker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Luca Jovine
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
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44
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Khan F, Suguna K. Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica. Acta Crystallogr F Struct Biol Commun 2019; 75:197-204. [PMID: 30839295 PMCID: PMC6404861 DOI: 10.1107/s2053230x19000499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/09/2019] [Indexed: 01/09/2023] Open
Abstract
ERGIC-53-like proteins are type I membrane proteins that belong to the class of intracellular cargo receptors and are known to be indispensable for the intracellular transport of glycoproteins. They are implicated in transporting glycoproteins between the endoplasmic reticulum and the Golgi body. The crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica has been determined at 2.4 Å resolution. Although the overall structure of the domain resembles those of its mammalian and yeast orthologs (ERGIC-53 and Emp46, respectively), there are significant changes in the carbohydrate-binding site. A sequence-based search revealed the presence of several homologs of ERGIC-53 in different species of Entamoeba. This is the first report of the structural characterization of a member of this class of proteins from a protozoan and serves to further knowledge and understanding regarding the species-specific differences.
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Affiliation(s)
- Farha Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
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45
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Gallego Del Sol F, Penadés JR, Marina A. Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems. Mol Cell 2019; 74:59-72.e3. [PMID: 30745087 PMCID: PMC6458997 DOI: 10.1016/j.molcel.2019.01.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 10/28/2022]
Abstract
Bacillus phages use a communication system, termed "arbitrium," to coordinate lysis-lysogeny decisions. Arbitrium communication is mediated by the production and secretion of a hexapeptide (AimP) during lytic cycle. Once internalized, AimP reduces the expression of the negative regulator of lysogeny, AimX, by binding to the transcription factor, AimR, promoting lysogeny. We have elucidated the crystal structures of AimR from the Bacillus subtilis SPbeta phage in its apo form, bound to its DNA operator and in complex with AimP. AimR presents intrinsic plasticity, sharing structural features with the RRNPP quorum-sensing family. Remarkably, AimR binds to an unusual operator with a long spacer that interacts nonspecifically with the receptor TPR domain, while the HTH domain canonically recognizes two inverted repeats. AimP stabilizes a compact conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the aimX promoter region. Our results establish the molecular basis of the arbitrium communication system.
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Affiliation(s)
- Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
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46
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Kenjić N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL. PvdF of pyoverdin biosynthesis is a structurally unique N 10-formyltetrahydrofolate-dependent formyltransferase. Arch Biochem Biophys 2019; 664:40-50. [PMID: 30689984 DOI: 10.1016/j.abb.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
Abstract
The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N10-formyltetrahydrofolate (N10-fTHF) as a co-substrate formyl donor to convert N5-hydroxyornithine (OHOrn) to N5-formyl- N5-hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N10-formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.
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Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA
| | - Carol A Caperelli
- Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.
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47
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Han X, Altegoer F, Steinchen W, Binnebesel L, Schuhmacher J, Glatter T, Giammarinaro PI, Djamei A, Rensing SA, Reissmann S, Kahmann R, Bange G. A kiwellin disarms the metabolic activity of a secreted fungal virulence factor. Nature 2019; 565:650-653. [PMID: 30651637 DOI: 10.1038/s41586-018-0857-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/04/2018] [Indexed: 01/01/2023]
Abstract
Fungi-induced plant diseases affect global food security and plant ecology. The biotrophic fungus Ustilago maydis causes smut disease in maize (Zea mays) plants by secreting numerous virulence effectors that reprogram plant metabolism and immune responses1,2. The secreted fungal chorismate mutase Cmu1 presumably affects biosynthesis of the plant immune signal salicylic acid by channelling chorismate into the phenylpropanoid pathway3. Here we show that one of the 20 maize-encoded kiwellins (ZmKWL1) specifically blocks the catalytic activity of Cmu1. ZmKWL1 hinders substrate access to the active site of Cmu1 through intimate interactions involving structural features that are specific to fungal Cmu1 orthologues. Phylogenetic analysis suggests that plant kiwellins have a versatile scaffold that can specifically counteract pathogen effectors such as Cmu1. We reveal the biological activity of a member of the kiwellin family, a widely conserved group of proteins that have previously been recognized only as important human allergens.
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Affiliation(s)
- Xiaowei Han
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Florian Altegoer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Wieland Steinchen
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Lynn Binnebesel
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Jan Schuhmacher
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pietro I Giammarinaro
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Armin Djamei
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan A Rensing
- Faculty of Biology, Philipps-University, Marburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stefanie Reissmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany.
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48
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Miller OK, Banfield MJ, Schwarz-Linek U. A new structural class of bacterial thioester domains reveals a slipknot topology. Protein Sci 2018; 27:1651-1660. [PMID: 30052296 PMCID: PMC6194298 DOI: 10.1002/pro.3478] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 11/11/2022]
Abstract
An increasing number of surface-associated proteins identified in Gram-positive bacteria are characterized by intramolecular cross-links in structurally conserved thioester, isopeptide, and ester domains (TIE proteins). Two classes of thioester domains (TEDs) have been predicted based on sequence with, to date, only representatives of Class I structurally characterized. Here, we present crystal structures of three Class II TEDs from Bacillus anthracis, vancomycin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecium. These proteins are structurally distinct from Class I TEDs due to a β-sandwich domain that is inserted into the conserved TED fold to form a slipknot structure. Further, the B. anthracis TED domain is presented in the context of a full-length sortase-anchored protein structure (BaTIE). This provides insight into the three-dimensional arrangement of TIE proteins, which emerge as very abundant putative adhesins of Gram-positive bacteria.
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Affiliation(s)
- Ona K Miller
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Mark J Banfield
- John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
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49
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Structure of ScpC, a virulence protease from Streptococcus pyogenes, reveals the functional domains and maturation mechanism. Biochem J 2018; 475:2847-2860. [DOI: 10.1042/bcj20180145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022]
Abstract
Group A Streptococcus (GAS; Streptococcus pyogenes) causes a wide range of infections, including pharyngitis, impetigo, and necrotizing fasciitis, and results in over half a million deaths annually. GAS ScpC (SpyCEP), a 180-kDa surface-exposed, subtilisin-like serine protease, acts as an essential virulence factor that helps S. pyogenes evade the innate immune response by cleaving and inactivating C-X-C chemokines. ScpC is thus a key candidate for the development of a vaccine against GAS and other pathogenic streptococcal species. Here, we report the crystal structures of full-length ScpC wild-type, the inactive mutant, and the ScpC–AEBSF inhibitor complex. We show ScpC to be a multi-domain, modular protein consisting of nine structural domains, of which the first five constitute the PR + A region required for catalytic activity. The four unique C-terminal domains of this protein are similar to collagen-binding and pilin proteins, suggesting an additional role for ScpC as an adhesin that might mediate the attachment of S. pyogenes to various host tissues. The Cat domain of ScpC is similar to subtilisin-like proteases with significant difference to dictate its specificity toward C-X-C chemokines. We further show that ScpC does not undergo structural rearrangement upon maturation. In the ScpC–inhibitor complex, the bound inhibitor breaks the hydrogen bond between active-site residues, which is essential for catalysis. Guided by our structure, we designed various epitopes and raised antibodies capable of neutralizing ScpC activity. Collectively, our results demonstrate the structure, maturation process, inhibition, and substrate recognition of GAS ScpC, and reveal the presence of functional domains at the C-terminal region.
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50
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The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Nat Commun 2018; 9:3266. [PMID: 30111885 PMCID: PMC6093860 DOI: 10.1038/s41467-018-05717-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
Complement component 9 (C9) functions as the pore-forming component of the Membrane Attack Complex (MAC). During MAC assembly, multiple copies of C9 are sequentially recruited to membrane associated C5b8 to form a pore. Here we determined the 2.2 Å crystal structure of monomeric murine C9 and the 3.9 Å resolution cryo EM structure of C9 in a polymeric assembly. Comparison with other MAC proteins reveals that the first transmembrane region (TMH1) in monomeric C9 is uniquely positioned and functions to inhibit its self-assembly in the absence of C5b8. We further show that following C9 recruitment to C5b8, a conformational change in TMH1 permits unidirectional and sequential binding of additional C9 monomers to the growing MAC. This mechanism of pore formation contrasts with related proteins, such as perforin and the cholesterol dependent cytolysins, where it is believed that pre-pore assembly occurs prior to the simultaneous release of the transmembrane regions.
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