1
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Witzenberger M, Janowski R, Niessing D. Crystal structure of the RNA-recognition motif of Drosophila melanogaster tRNA (uracil-5-)-methyltransferase homolog A. Acta Crystallogr F Struct Biol Commun 2024; 80:36-42. [PMID: 38270511 PMCID: PMC10836426 DOI: 10.1107/s2053230x24000645] [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: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neurodegenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and polyQ protein aggregation, suggesting this protein as a valid drug target against this class of disorders. In this paper, the 1.6 Å resolution crystal structure of the RNA-recognition motif (RRM) from Drosophila melanogaster, which is a homolog of human TRMT2A, is described and analysed.
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Affiliation(s)
- Monika Witzenberger
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Munich, Germany
| | - Robert Janowski
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Munich, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Munich, Germany
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2
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Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [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: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
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3
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Usón I, Sheldrick GM. Modes and model building in SHELXE. Acta Crystallogr D Struct Biol 2024; 80:4-15. [PMID: 38088896 PMCID: PMC10833347 DOI: 10.1107/s2059798323010082] [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: 10/01/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024] Open
Abstract
Density modification is a standard step to provide a route for routine structure solution by any experimental phasing method, with single-wavelength or multi-wavelength anomalous diffraction being the most popular methods, as well as to extend fragments or incomplete models into a full solution. The effect of density modification on the starting maps from either source is illustrated in the case of SHELXE. The different modes in which the program can run are reviewed; these include less well known uses such as reading external phase values and weights or phase distributions encoded in Hendrickson-Lattman coefficients. Typically in SHELXE, initial phases are calculated from experimental data, from a partial model or map, or from a combination of both sources. The initial phase set is improved and extended by density modification and, if the resolution of the data and the type of structure permits, polyalanine tracing. As a feature to systematically eliminate model bias from phases derived from predicted models, the trace can be set to exclude the area occupied by the starting model. The trace now includes an extension into the gamma position or hydrophobic and aromatic side chains if a sequence is provided, which is performed in every tracing cycle. Once a correlation coefficient of over 30% between the structure factors calculated from such a trace and the native data indicates that the structure has been solved, the sequence is docked in all model-building cycles and side chains are fitted if the map supports it. The extensions to the tracing algorithm brought in to provide a complete model are discussed. The improvement in phasing performance is assessed using a set of tests.
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Affiliation(s)
- Isabel Usón
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, Barcelona, E-08003, Spain
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixach, 15, Barcelona, 08028, Spain
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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4
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Brehm W, Triviño J, Krahn JM, Usón I, Diederichs K. XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J Appl Crystallogr 2023; 56:1585-1594. [PMID: 37791359 PMCID: PMC10543682 DOI: 10.1107/s1600576723007057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
XDSGUI is a lightweight graphical user interface (GUI) for the XDS, SHELX and ARCIMBOLDO program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X-ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user-modifiable and user-extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.
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Affiliation(s)
- Wolfgang Brehm
- Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Josep Triviño
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz 78457, Germany
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Shi H, Panjikar S, Li C, Ou X, Zhou Y, Zhang K, Song L, Yu R, Sun L, Zhu J. Characterization of a novel recombinant calcium-binding protein from Arca subcrenata and its anti-hepatoma activities in vitro and in vivo. Int J Biol Macromol 2023; 245:125513. [PMID: 37353116 DOI: 10.1016/j.ijbiomac.2023.125513] [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: 02/08/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Previous studies demonstrated that ASP-3 was a novel calcium-binding protein from Arca subcrenata that effectively inhibited the proliferation of HepG2 cells. To further study the antitumor activity and mechanism of ASP-3, the cytotoxic effects of recombinant ASP-3 were evaluated in HepG2 cells. The results demonstrated that ASP-3 inhibited the proliferation of HepG2 cells by competitively binding to the EGF binding pocket of EGFR and inhibiting the JAK-STAT, RAS-RAF-MEK-ERK, and PI3K-Akt-mTOR signaling pathways mediated by EGFR. ASP-3 significantly inhibited tumor growth in a HepG2 cell subcutaneous xenograft nude mouse model, and its (25 mg/kg and 75 mg/kg) tumor inhibition rates were 46.92 % and 60.28 %, respectively. Furthermore, the crystal structure of ASP-3 was resolved at 1.4 Å. ASP-3 formed as a stable dimer and folded as an EF-Hand structure. ASP-3 stably bound to domain I and domain III of the EGFR extracellular region by using molecular docking and molecular dynamics simulation analysis. Compared with the endogenous ligand EGF, ASP-3 displayed a stronger interaction with EGFR. These experimental results indicated that recombinant ASP-3 possessed an effective anti-hepatoma effect. So, it might be a potential molecule for liver cancer therapy.
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Affiliation(s)
- Hui Shi
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | | | - Chunlei Li
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Xiaozheng Ou
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Yun Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kunhao Zhang
- Department of Life Science, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Liyan Song
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Rongmin Yu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianhua Zhu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
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6
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Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M. Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Nat Commun 2023; 14:4233. [PMID: 37454201 PMCID: PMC10349855 DOI: 10.1038/s41467-023-39961-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains to cis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.
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Affiliation(s)
- Komal Soni
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sophie Bonnal
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Arie Geerlof
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Ralf Stehle
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany.
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7
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Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
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Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
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8
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Natashin PV, Burakova LP, Kovaleva MI, Shevtsov MB, Dmitrieva DA, Eremeeva EV, Markova SV, Mishin AV, Borshchevskiy VI, Vysotski ES. The Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study. Int J Mol Sci 2023; 24:ijms24076869. [PMID: 37047842 PMCID: PMC10095345 DOI: 10.3390/ijms24076869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca2+-discharged photoproteins). Moreover, we determined the spatial structure of the obelin mutant with a substitution of His64, the key residue of the presumable proton transfer, to Phe. On the ground of the bioluminescence properties of the obelin and aequorin mutants as well as the spatial structures of the obelin mutants with the replacements of His64 and Tyr138, the conclusion was made that, in fact, His residue of the Tyr-His-Trp triad and the water molecule perform the "catalytic function" by transferring the proton from solvent to the dioxetanone anion to generate its neutral ionic state in complex with water, as only the decomposition of this form of dioxetanone can provide the highest light output in the light-emitting reaction of the hydromedusan photoproteins.
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Affiliation(s)
- Pavel V Natashin
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
| | - Ludmila P Burakova
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Margarita I Kovaleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Mikhail B Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Elena V Eremeeva
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Svetlana V Markova
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
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9
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Chang TH, Hsieh FL, Gu X, Smallwood PM, Kavran JM, Gabelli SB, Nathans J. Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Proc Natl Acad Sci U S A 2023; 120:e2221103120. [PMID: 36996108 PMCID: PMC10083539 DOI: 10.1073/pnas.2221103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low-molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration-presumably a coiled coil-held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP-i.e., the long dimension of the pore-and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.
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Affiliation(s)
- Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Xiaowu Gu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Philip M. Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jennifer M. Kavran
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
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10
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Hor L, Pilapitiya A, McKenna JA, Panjikar S, Anderson MA, Desvaux M, Paxman JJ, Heras B. Crystal structure of a subtilisin-like autotransporter passenger domain reveals insights into its cytotoxic function. Nat Commun 2023; 14:1163. [PMID: 36859523 PMCID: PMC9977779 DOI: 10.1038/s41467-023-36719-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023] Open
Abstract
Autotransporters (ATs) are a large family of bacterial secreted and outer membrane proteins that encompass a wide range of enzymatic activities frequently associated with pathogenic phenotypes. We present the structural and functional characterisation of a subtilase autotransporter, Ssp, from the opportunistic pathogen Serratia marcescens. Although the structures of subtilases have been well documented, this subtilisin-like protein is associated with a 248 residue β-helix and itself includes three finger-like protrusions around its active site involved in substrate interactions. We further reveal that the activity of the subtilase AT is required for entry into epithelial cells as well as causing cellular toxicity. The Ssp structure not only provides details about the subtilase ATs, but also reveals a common framework and function to more distantly related ATs. As such these findings also represent a significant step forward toward understanding the molecular mechanisms underlying the functional divergence in the large AT superfamily.
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Affiliation(s)
- Lilian Hor
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Akila Pilapitiya
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - James A McKenna
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Mickaël Desvaux
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000, Clermont-Ferrand, France
| | - Jason J Paxman
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia.
| | - Begoña Heras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia.
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11
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Traore DAK, Torres VVL, Akhtar N, Gummer AM, Flanigan SF, Coulibaly F, Adams V, Whisstock JC, Rood JI. TcpA from the Clostridiumperfringens plasmid pCW3 is more closely related to the DNA translocase FtsK than to coupling proteins. Structure 2023; 31:455-463.e4. [PMID: 36841236 DOI: 10.1016/j.str.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/17/2022] [Accepted: 01/31/2023] [Indexed: 02/27/2023]
Abstract
Conjugative DNA transfer is a major factor in the dissemination of antibiotic resistance and virulence genes. In the Gram-positive pathogen Clostridium perfringens, the majority of conjugative plasmids share the conserved tcp locus that governs the assembly of the transfer system. Here, we describe multiple structures of the coupling protein TcpA, an essential ATPase that is suggested to provide the mechanical force to propel the DNA through the transfer apparatus. The structures of TcpA in the presence and absence of nucleotides revealed conformational rearrangements and highlight a crucial role for the unstructured C terminus. Our findings reveal that TcpA shares most structural similarity with the FtsK DNA translocase, a central component of the bacterial cell division machinery. Our structural data suggest that conjugation in C. perfringens may have evolved from the bacterial chromosome segregation system and, accordingly, suggest the possibility that double-stranded DNA is transferred through the Tcp conjugation apparatus.
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Affiliation(s)
- Daouda A K Traore
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako (USTTB), Bamako, Mali; Faculty of Natural Sciences, School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK; Life Sciences Group, Institut Laue Langevin, Grenoble, France.
| | - Von Vergel L Torres
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Infection Program, Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Naureen Akhtar
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Alexandra M Gummer
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sarena F Flanigan
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Fasséli Coulibaly
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Vicki Adams
- Infection Program, Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - James C Whisstock
- Infection Program, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Julian I Rood
- Infection Program, Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
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12
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Kim CY, Mitchell AJ, Kastner DW, Albright CE, Gutierrez MA, Glinkerman CM, Kulik HJ, Weng JK. Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY. Nat Commun 2023; 14:597. [PMID: 36737607 PMCID: PMC9898226 DOI: 10.1038/s41467-023-36299-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Plants contain rapidly evolving specialized enzymes that support the biosynthesis of functionally diverse natural products. In coumarin biosynthesis, a BAHD acyltransferase-family enzyme COSY was recently discovered to accelerate coumarin formation as the only known BAHD enzyme to catalyze an intramolecular acyl transfer reaction. Here we investigate the structural and mechanistic basis for COSY's coumarin synthase activity. Our structural analyses reveal an unconventional active-site configuration adapted to COSY's specialized activity. Through mutagenesis studies and deuterium exchange experiments, we identify a unique proton exchange mechanism at the α-carbon of the o-hydroxylated trans-hydroxycinnamoyl-CoA substrates during the catalytic cycle of COSY. Quantum mechanical cluster modeling and molecular dynamics further support this key mechanism for lowering the activation energy of the rate-limiting trans-to-cis isomerization step in coumarin production. This study unveils an unconventional catalytic mechanism mediated by a BAHD-family enzyme, and sheds light on COSY's evolutionary origin and its recruitment to coumarin biosynthesis in eudicots.
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Affiliation(s)
- Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - David W Kastner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claire E Albright
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | | | | | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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13
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Natashin PV, Eremeeva EV, Shevtsov MB, Kovaleva MI, Bukhdruker SS, Dmitrieva DA, Gulnov DV, Nemtseva EV, Gordeliy VI, Mishin AV, Borshchevskiy VI, Vysotski ES. Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product. Sci Rep 2022; 12:19613. [PMID: 36379962 PMCID: PMC9666459 DOI: 10.1038/s41598-022-24117-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, Ca2+-regulated photoproteins activated with CTZ-v display very low bioluminescence activities that hampers its usage as a substrate of photoprotein bioluminescence. Here, we report the crystal structure of semi-synthetic Ca2+-discharged obelin-v bound with the reaction product determined at 2.1 Å resolution. Comparison of the crystal structure of Ca2+-discharged obelin-v with those of other obelins before and after bioluminescence reaction reveals no considerable changes in the overall structure. However, the drastic changes in CTZ-binding cavity are observed owing to the completely different reaction product, coelenteramine-v (CTM-v). Since CTM-v is certainly the main product of obelin-v bioluminescence and is considered to be a product of the "dark" pathway of dioxetanone intermediate decomposition, it explains the low bioluminescence activity of obelin and apparently of other photoproteins with CTZ-v.
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Affiliation(s)
- Pavel V. Natashin
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
| | - Elena V. Eremeeva
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia ,grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Mikhail B. Shevtsov
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Margarita I. Kovaleva
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey S. Bukhdruker
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria A. Dmitrieva
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitry V. Gulnov
- grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Elena V. Nemtseva
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia ,grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Valentin I. Gordeliy
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France ,grid.1957.a0000 0001 0728 696XInstitute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Alexey V. Mishin
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin I. Borshchevskiy
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia ,grid.33762.330000000406204119Joint Institute for Nuclear Research, Dubna, Russia
| | - Eugene S. Vysotski
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
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14
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Kiliszek A, Pluta M, Bejger M, Rypniewski W. Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair. RNA (NEW YORK, N.Y.) 2022; 29:rna.079414.122. [PMID: 36319090 PMCID: PMC9808570 DOI: 10.1261/rna.079414.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.
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15
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Hou Y, Höppner A, Rao AG, Lahav Y, Kumar Das P, Ding W, Jiang X, Hu J, Schapiro I, Noy D, Zhao K. Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin. Protein Sci 2022. [DOI: 10.1002/pro.4412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ya‐Nan Hou
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Astrid Höppner
- Center for Structural Studies Heinrich‐Heine‐Universität Düsseldorf Germany
| | - Aditya G. Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
| | - Yigal Lahav
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
| | - Prabir Kumar Das
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
| | - Wen‐Long Ding
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Xiang‐Xiang Jiang
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Ji‐Ling Hu
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
| | - Dror Noy
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
- Faculty of Sciences and Technology Tel‐Hai Academic College Upper Galilee Israel
| | - Kai‐Hong Zhao
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
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16
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Di Fiore A, De Luca V, Langella E, Nocentini A, Buonanno M, Maria Monti S, Supuran CT, Capasso C, De Simone G. Biochemical, structural, and computational studies of a γ-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei. Comput Struct Biotechnol J 2022; 20:4185-4194. [PMID: 36016712 PMCID: PMC9389205 DOI: 10.1016/j.csbj.2022.07.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Melioidosis is a severe disease caused
Burkholderia pseudomallei. γ-carbonic anhydrases (γ-CAs) have been recently
introduced as novel antibacterial drug targets. A new γ-CA from B.
pseudomallei has been investigated by a
multidisciplinary approach. Obtained results provide an important starting point
for developing new anti-melioidosis drugs.
Melioidosis is a severe disease caused by the highly
pathogenic gram-negative bacterium Burkholderia
pseudomallei. Several studies have highlighted the broad
resistance of this pathogen to many antibiotics and pointed out the pivotal
importance of improving the pharmacological arsenal against it. Since γ-carbonic
anhydrases (γ-CAs) have been recently introduced as potential and novel
antibacterial drug targets, in this paper, we report a detailed characterization
of BpsγCA, a γ-CA from B.
pseudomallei by a multidisciplinary approach. In
particular, the enzyme was recombinantly produced and biochemically
characterized. Its catalytic activity at different pH values was measured, the
crystal structure was determined and theoretical pKa calculations were carried
out. Results provided a snapshot of the enzyme active site and dissected the
role of residues involved in the catalytic mechanism and ligand recognition.
These findings are an important starting point for developing new
anti-melioidosis drugs targeting BpsγCA.
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17
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Jäger F, Lamy A, Sun WS, Guerini N, Berntsson RPA. Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family. Structure 2022; 30:876-885.e5. [DOI: 10.1016/j.str.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
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18
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Patel O, Brammananth R, Dai W, Panjikar S, Coppel RL, Lucet IS, Crellin PK. Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis. Acta Crystallogr D Struct Biol 2022; 78:494-508. [PMID: 35362472 PMCID: PMC8972800 DOI: 10.1107/s2059798322001772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one-quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl-myo-inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface-exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full-length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities and one α-helix extending away from the β-barrel core, resembling a `cone with a flake' arrangement. Through xenon derivatization and structural comparison with AlphaFold2-derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from `closed' to `open' conformations, allowing cavity access. An AlphaFold2-derived NCgl2760 model predicted a smaller β-barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis.
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Affiliation(s)
- Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Rajini Brammananth
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Weiwen Dai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Victoria 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Victoria 3800, Australia
| | - Ross L. Coppel
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Isabelle S. Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Paul K. Crellin
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
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19
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Margreiter MA, Witzenberger M, Wasser Y, Davydova E, Janowski R, Metz J, Habib P, Sahnoun SEM, Sobisch C, Poma B, Palomino-Hernandez O, Wagner M, Carell T, Jon Shah N, Schulz JB, Niessing D, Voigt A, Rossetti G. Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death. Comput Struct Biotechnol J 2022; 20:443-458. [PMID: 35070167 PMCID: PMC8759985 DOI: 10.1016/j.csbj.2021.12.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
Polyglutamine (polyQ) diseases are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster. This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases in humans. Computer-aided drug discovery was implemented to identify human TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined, and Biacore experiments with the RRM were performed. The identified molecules were validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Our work provides a first step towards pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.
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Affiliation(s)
- Michael A Margreiter
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
| | - Monika Witzenberger
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Yasmine Wasser
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Elena Davydova
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Robert Janowski
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Jonas Metz
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany
| | - Pardes Habib
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany
| | - Sabri E M Sahnoun
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Carina Sobisch
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Benedetta Poma
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Oscar Palomino-Hernandez
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
| | - Mirko Wagner
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 München, Germany
| | - Thomas Carell
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 München, Germany
| | - N Jon Shah
- JARA - BRAIN - Translational Medicine, Aachen, Germany.,Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Juelich GmbH, Germany.,Institute of Neuroscience and Medicine (INM-11), Forschungszentrum Juelich GmbH, Germany
| | - Jörg B Schulz
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Institute of Neuroscience and Medicine (INM-11), Forschungszentrum Juelich GmbH, Germany
| | - Dierk Niessing
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Aaron Voigt
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,Juelich Supercomputing Center (JSC), Forschungszentrum Juelich GmbH, Germany.,Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
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20
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Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W. The induction mechanism of the flavonoid-responsive regulator FrrA. FEBS J 2022; 289:507-518. [PMID: 34314575 DOI: 10.1111/febs.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation-promoting genetic programme in the presence of host-produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid-responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR-like fold whose DNA-binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C-H contacts to the π-system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA-binding domain and the absence of structural change upon ligand binding are corroborated by small-angle X-ray scattering (SAXS) experiments in solution. Together with a model of the promoter-bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA-binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.
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Affiliation(s)
- Nadine Werner
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Sebastiaan Werten
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Jens Hoppen
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Gottfried J Palm
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Michael Göttfert
- Institute of Genetics, Dresden University of Technology, Germany
| | - Winfried Hinrichs
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
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21
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Mahto JK, Neetu N, Waghmode B, Kuatsjah E, Sharma M, Sircar D, Sharma AK, Tomar S, Eltis LD, Kumar P. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J Biol Chem 2021; 297:101416. [PMID: 34800435 PMCID: PMC8649396 DOI: 10.1016/j.jbc.2021.101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDOKF1 from Comamonas testosteroni KF1 and found that it had an apparent kcat/Km for phthalate of 0.58 ± 0.09 μM-1s-1, over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDOKF1 larger than that of other characterized ROs. Complexes of PDOKF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.
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Affiliation(s)
- Jai Krishna Mahto
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Eugene Kuatsjah
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Monica Sharma
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Shailly Tomar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
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22
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Li K, Zheng J, Wirawan M, Trinh NM, Fedorova O, Griffin PR, Pyle AM, Luo D. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Res 2021; 49:9978-9991. [PMID: 34403472 PMCID: PMC8464030 DOI: 10.1093/nar/gkab712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
DRH-3 is critically involved in germline development and RNA interference (RNAi) facilitated chromosome segregation via the 22G-siRNA pathway in Caenorhabditis elegans. DRH-3 has similar domain architecture to RIG-I-like receptors (RLRs) and belongs to the RIG-I-like RNA helicase family. The molecular understanding of DRH-3 and its function in endogenous RNAi pathways remains elusive. In this study, we solved the crystal structures of the DRH-3 N-terminal domain (NTD) and the C-terminal domains (CTDs) in complex with 5'-triphosphorylated RNAs. The NTD of DRH-3 adopts a distinct fold of tandem caspase activation and recruitment domains (CARDs) structurally similar to the CARDs of RIG-I and MDA5, suggesting a signaling function in the endogenous RNAi biogenesis. The CTD preferentially recognizes 5'-triphosphorylated double-stranded RNAs bearing the typical features of secondary siRNA transcripts. The full-length DRH-3 displays unique structural dynamics upon binding to RNA duplexes that differ from RIG-I or MDA5. These features of DRH-3 showcase the evolutionary divergence of the Dicer and RLR family of helicases.
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Affiliation(s)
- Kuohan Li
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Jie Zheng
- The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Nguyen Mai Trinh
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
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23
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Subedi P, Paxman JJ, Wang G, Hor L, Hong Y, Verderosa AD, Whitten AE, Panjikar S, Santos-Martin CF, Martin JL, Totsika M, Heras B. Salmonella enterica BcfH Is a Trimeric Thioredoxin-Like Bifunctional Enzyme with Both Thiol Oxidase and Disulfide Isomerase Activities. Antioxid Redox Signal 2021; 35:21-39. [PMID: 33607928 DOI: 10.1089/ars.2020.8218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aims: Thioredoxin (TRX)-fold proteins are ubiquitous in nature. This redox scaffold has evolved to enable a variety of functions, including redox regulation, protein folding, and oxidative stress defense. In bacteria, the TRX-like disulfide bond (Dsb) family mediates the oxidative folding of multiple proteins required for fitness and pathogenic potential. Conventionally, Dsb proteins have specific redox functions with monomeric and dimeric Dsbs exclusively catalyzing thiol oxidation and disulfide isomerization, respectively. This contrasts with the eukaryotic disulfide forming machinery where the modular TRX protein disulfide isomerase (PDI) mediates thiol oxidation and disulfide reshuffling. In this study, we identified and structurally and biochemically characterized a novel Dsb-like protein from Salmonella enterica termed bovine colonization factor protein H (BcfH) and defined its role in virulence. Results: In the conserved bovine colonization factor (bcf) fimbrial operon, the Dsb-like enzyme BcfH forms a trimeric structure, exceptionally uncommon among the large and evolutionary conserved TRX superfamily. This protein also displays very unusual catalytic redox centers, including an unwound α-helix holding the redox active site and a trans-proline instead of the conserved cis-proline active site loop. Remarkably, BcfH displays both thiol oxidase and disulfide isomerase activities contributing to Salmonella fimbrial biogenesis. Innovation and Conclusion: Typically, oligomerization of bacterial Dsb proteins modulates their redox function, with monomeric and dimeric Dsbs mediating thiol oxidation and disulfide isomerization, respectively. This study demonstrates a further structural and functional malleability in the TRX-fold protein family. BcfH trimeric architecture and unconventional catalytic sites permit multiple redox functions emulating in bacteria the eukaryotic PDI dual oxidoreductase activity. Antioxid. Redox Signal. 35, 21-39.
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Affiliation(s)
- Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lilian Hor
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Anthony D Verderosa
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia
| | - Santosh Panjikar
- Macromolecular Crystallography, Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Carlos F Santos-Martin
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Brisbane Innovation Park, Nathan, Australia.,Vice-Chancellor's Unit, University of Wollongong, Wollongong, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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24
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Krska D, Mazurkewich S, Brown HA, Theibich Y, Poulsen JCN, Morris AL, Koropatkin NM, Lo Leggio L, Larsbrink J. Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii. Biochemistry 2021; 60:2206-2220. [PMID: 34180241 PMCID: PMC8280721 DOI: 10.1021/acs.biochem.1c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, CkXyn10C-GE15A, which
incorporates two catalytic domains, a xylanase and a glucuronoyl esterase,
and five carbohydrate-binding modules (CBMs) from families 9 and 22.
The xylanase and glucuronoyl esterase catalytic domains were recently
biochemically characterized, as was the ability of the individual
CBMs to bind insoluble polysaccharides. Here, we further probed the
abilities of the different CBMs from CkXyn10C-GE15A
to bind to soluble poly- and oligosaccharides using affinity gel electrophoresis,
isothermal titration calorimetry, and differential scanning fluorimetry.
The results revealed additional binding properties of the proteins
compared to the former studies on insoluble polysaccharides. Collectively,
the results show that all five CBMs have their own distinct binding
preferences and appear to complement each other and the catalytic
domains in targeting complex cell wall polysaccharides. Additionally,
through renewed efforts, we have achieved partial structural characterization
of this complex multidomain protein. We have determined the structures
of the third CBM9 domain (CBM9.3) and the glucuronoyl esterase (GE15A)
by X-ray crystallography. CBM9.3 is the second CBM9 structure determined
to date and was shown to bind oligosaccharide ligands at the same
site but in a different binding mode compared to that of the previously
determined CBM9 structure from Thermotoga maritima. GE15A represents a unique intermediate between reported fungal
and bacterial glucuronoyl esterase structures as it lacks two inserted
loop regions typical of bacterial enzymes and a third loop has an
atypical structure. We also report small-angle X-ray scattering measurements
of the N-terminal CBM22.1–CBM22.2–Xyn10C construct,
indicating a compact arrangement at room temperature.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yusuf Theibich
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | | | - Adeline L Morris
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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25
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Werner N, Petersen K, Vollstedt C, Garcia PP, Chow J, Ferrer M, Fernandez-Lopez L, Falke S, Perbandt M, Hinrichs W, Betzel C, Streit WR. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. Sci Rep 2021; 11:12255. [PMID: 34112823 PMCID: PMC8192741 DOI: 10.1038/s41598-021-91536-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 11/09/2022] Open
Abstract
Previously, we reported the isolation of a quorum quenching protein (QQ), designated GqqA, from Komagataeibacter europaeus CECT 8546 that is highly homologous to prephenate dehydratases (PDT) (Valera et al. in Microb Cell Fact 15, 88. https://doi.org/10.1186/s12934-016-0482-y , 2016). GqqA strongly interfered with N-acyl-homoserine lactone (AHL) quorum sensing signals from Gram-negative bacteria and affected biofilm formation in its native host strain Komagataeibacter europaeus. Here we present and discuss data identifying GqqA as a novel acylase. ESI-MS-MS data showed unambiguously that GqqA hydrolyzes the amide bond of the acyl side-chain of AHL molecules, but not the lactone ring. Consistent with this observation the protein sequence does not carry a conserved Zn2+ binding motif, known to be essential for metal-dependent lactonases, but in fact harboring the typical periplasmatic binding protein domain (PBP domain), acting as catalytic domain. We report structural details for the native structure at 2.5 Å resolution and for a truncated GqqA structure at 1.7 Å. The structures obtained highlight that GqqA acts as a dimer and complementary docking studies indicate that the lactone ring of the substrate binds within a cleft of the PBP domain and interacts with polar residues Y16, S17 and T174. The biochemical and phylogenetic analyses imply that GqqA represents the first member of a novel type of QQ family enzymes.
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Affiliation(s)
- Nadine Werner
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Katrin Petersen
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Christel Vollstedt
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Pablo Perez Garcia
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Jennifer Chow
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Laura Fernandez-Lopez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Markus Perbandt
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Winfried Hinrichs
- Institute for Biochemistry, University Greifswald, 17487, Greifswald, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany.
| | - Wolfgang R Streit
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany.
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26
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Kolenko P, Stránský J, Koval' T, Malý M, Dohnálek J. SHELIXIR: automation of experimental phasing procedures using SHELXC/ D/ E. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721002454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The program SHELIXIR represents a simple and efficient tool for routine phase-problem solution using data for experimental phasing by the single-wavelength anomalous dispersion, multiwavelength anomalous dispersion, single isomorphous replacement with anomalous scattering and radiation-damage-induced phasing methods. As indicated in its name, all calculation procedures are performed with the SHELXC/D/E program package. SHELIXIR provides screening for alternative space groups, optimal solvent content, and high- and low-resolution limits. The procedures of SHELXE are parallelized to minimize the computational time. The automation and parallelization of such procedures are suitable for phasing at synchrotron beamlines directly or for finding the optimal parameters for further data processing. A simple graphical interface is designed to make use easier and to increase efficiency during beam time.
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27
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Keough DT, Wun SJ, Baszczyňski O, Eng WS, Špaček P, Panjikar S, Naesens L, Pohl R, Rejman D, Hocková D, Ferrero RL, Guddat LW. Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections. J Med Chem 2021; 64:5710-5729. [PMID: 33891818 DOI: 10.1021/acs.jmedchem.0c02184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori (Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world's population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine-guanine-hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with Ki values as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[(N-3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Shun Jie Wun
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Wai Soon Eng
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton 3168, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Lieve Naesens
- Katholieke Universiteit, Leuven, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Richard L Ferrero
- Hudson Institute of Medical Research, Clayton 3800, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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28
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Teixeira RD, Holzschuh F, Schirmer T. Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase. Nat Commun 2021; 12:2162. [PMID: 33846343 PMCID: PMC8041772 DOI: 10.1038/s41467-021-22492-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/15/2021] [Indexed: 01/24/2023] Open
Abstract
Diguanylate cyclases synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain, but how activation proceeds mechanistically is, apart from a few examples, still largely unknown. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR from Leptospira biflexa is a constitutively dimeric prototype of this class of diguanylate cyclases. Full-length crystal structures reveal that BeF3- pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coil via a localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many diguanylate cyclases with N-terminal coiled-coil linkers. As part of two-component systems, diguanylate cyclases (DGCs) are activated by phosphorylation. Structural and computational analyses of DgcR, a model DGC, reveal the phosphorylation-induced conformational changes and the activation mechanism likely shared by many DGCs with N-terminal coiled-coil linkers.
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Affiliation(s)
| | - Fabian Holzschuh
- Structural Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Structural Biology, Biozentrum, University of Basel, Basel, Switzerland.
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29
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Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution. Biochem J 2021; 477:3951-3962. [PMID: 33000863 DOI: 10.1042/bcj20200529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 09/30/2020] [Indexed: 11/17/2022]
Abstract
Snake venoms are complex mixtures of enzymes and nonenzymatic proteins that have evolved to immobilize and kill prey animals or deter predators. Among them, three-finger toxins (3FTxs) belong to the largest superfamily of nonenzymatic proteins. They share a common structure of three β-stranded loops extending like fingers from a central core containing all four conserved disulfide bonds. Most 3FTxs are monomers and through subtle changes in their amino acid sequences, they interact with different receptors, ion channels and enzymes to exhibit a wide variety of biological effects. The 3FTxs have further expanded their pharmacological space through covalent or noncovalent dimerization. Synergistic-type toxins (SynTxs) isolated from the deadly mamba venoms, although nontoxic, have been known to enhance the toxicity of other venom proteins. However, the details of three-dimensional structure and molecular mechanism of activity of this unusual class of 3FTxs are unclear. We determined the first three-dimensional structure of a SynTx isolated from Dendroaspis jamesoni jamesoni (Jameson's mamba) venom. The SynTx forms a unique homodimer that is held together by an interchain disulfide bond. The dimeric interface is elaborate and encompasses loops II and III. In addition to the inter-subunit disulfide bond, the hydrogen bonds and hydrophobic interactions between the monomers contribute to the dimer formation. Besides, two sulfate ions that mediate interactions between the monomers. This unique quaternary structure is evolved through noncovalent homodimers such as κ-bungarotoxins. This novel dimerization further enhances the diversity in structure and function of 3FTxs.
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Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Proc Natl Acad Sci U S A 2021; 118:2020393118. [PMID: 33619097 PMCID: PMC7936274 DOI: 10.1073/pnas.2020393118] [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: 11/23/2022] Open
Abstract
Bacterial noncoding RNAs (ncRNAs) play key roles in many biological processes including gene regulation, RNA processing and modification, and protein synthesis and translocation. OLE RNAs, found in many Gram-positive species, are one of the largest highly structured ncRNA classes whose biochemical functions remain unknown. In Bacillus halodurans, OLE RNAs interact with at least two proteins, OapA and OapB, which are required to assemble a functional OLE ribonucleoprotein (RNP) complex contributing to cellular responses to certain environmental stresses. We established X-ray structural models that reveal the sequence elements and tertiary structural features of OLE RNA that are critical for its specific recognition by OapB, which will aid future exploration of the biological and biochemical functions of the unusual OLE RNP complex. The OLE (ornate, large, and extremophilic) RNA class is one of the most complex and well-conserved bacterial noncoding RNAs known to exist. This RNA is known to be important for bacterial responses to stress caused by short-chain alcohols, cold, and elevated Mg2+ concentrations. These biological functions have been shown to require the formation of a ribonucleoprotein (RNP) complex including at least two protein partners: OLE-associated protein A (OapA) and OLE-associated protein B (OapB). OapB directly binds OLE RNA with high-affinity and specificity and is believed to assist in assembling the functional OLE RNP complex. To provide the atomic details of OapB–OLE RNA interaction and to potentially reveal previously uncharacterized protein–RNA interfaces, we determined the structure of OapB from Bacillus halodurans alone and in complex with an OLE RNA fragment at resolutions of 1.0 Å and 2.0 Å, respectively. The structure of OapB exhibits a K-shaped overall architecture wherein its conserved KOW motif and additional unique structural elements of OapB form a bipartite RNA-binding surface that docks to the P13 hairpin and P12.2 helix of OLE RNA. These high-resolution structures elucidate the molecular contacts used by OapB to form a stable RNP complex and explain the high conservation of sequences and structural features at the OapB–OLE RNA-binding interface. These findings provide insight into the role of OapB in the assembly and biological function of OLE RNP complex and can guide the exploration of additional possible OLE RNA-binding interactions present in OapB.
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Kmezik C, Mazurkewich S, Meents T, McKee LS, Idström A, Armeni M, Savolainen O, Brändén G, Larsbrink J. A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. J Biol Chem 2021; 296:100500. [PMID: 33667545 PMCID: PMC8040265 DOI: 10.1016/j.jbc.2021.100500] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomke Meents
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden
| | - Alexander Idström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marina Armeni
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden.
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Urbański LJ, Di Fiore A, Azizi L, Hytönen VP, Kuuslahti M, Buonanno M, Monti SM, Angeli A, Zolfaghari Emameh R, Supuran CT, De Simone G, Parkkila S. Biochemical and structural characterisation of a protozoan beta-carbonic anhydrase from Trichomonas vaginalis. J Enzyme Inhib Med Chem 2021; 35:1292-1299. [PMID: 32515610 PMCID: PMC7717681 DOI: 10.1080/14756366.2020.1774572] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We report the biochemical and structural characterisation of a beta-carbonic anhydrase (β-CA) from Trichomonas vaginalis, a unicellular parasite responsible for one of the world’s leading sexually transmitted infections, trichomoniasis. CAs are ubiquitous metalloenzymes belonging to eight evolutionarily divergent groups (α, β, γ, δ, ζ, η, θ, and ι); humans express only α-CAs, whereas many clinically significant pathogens express only β- and/or γ-CAs. For this reason, the latter two groups of CAs are promising biomedical targets for novel antiinfective agents. The β-CA from T. vaginalis (TvaCA1) was recombinantly produced and biochemically characterised. The crystal structure was determined, revealing the canonical dimeric fold of β-CAs and the main features of the enzyme active site. The comparison with the active site of human CA enzymes revealed significant differences that can be exploited for the design of inhibitors selective for the protozoan enzyme with respect to the human ones.
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Affiliation(s)
- Linda J Urbański
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna Di Fiore
- Institute of Biostructures and Bioimaging of the National Research Council, Naples, Italy
| | - Latifeh Azizi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd, Tampere, Finland
| | - Marianne Kuuslahti
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Martina Buonanno
- Institute of Biostructures and Bioimaging of the National Research Council, Naples, Italy
| | - Simona M Monti
- Institute of Biostructures and Bioimaging of the National Research Council, Naples, Italy
| | - Andrea Angeli
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Claudiu T Supuran
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Giuseppina De Simone
- Institute of Biostructures and Bioimaging of the National Research Council, Naples, Italy
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd, Tampere, Finland
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Chojnowski G, Sobolev E, Heuser P, Lamzin VS. The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP. Acta Crystallogr D Struct Biol 2021; 77:142-150. [PMID: 33559604 PMCID: PMC7869898 DOI: 10.1107/s2059798320016332] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/16/2020] [Indexed: 11/26/2022] Open
Abstract
A new module of the ARP/wARP suite for automated model building into cryo-EM maps is presented. Recent developments in cryogenic electron microscopy (cryo-EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high-resolution cryo-EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo-EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main-chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo-EM maps is comparable to that of X-ray crystallographic models at similar local cryo-EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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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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Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity. Sci Rep 2020; 10:17398. [PMID: 33060678 PMCID: PMC7562740 DOI: 10.1038/s41598-020-74332-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/21/2020] [Indexed: 12/02/2022] Open
Abstract
Plantacyclin B21AG is a circular bacteriocin produced by Lactiplantibacillus plantarum B21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens, Listeria monocytogenes and Clostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from a food grade Lactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 18 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed that Phe8Ala and Trp45Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. The Lys19Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the relative importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
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Diversity in the intrinsic apoptosis pathway of nematodes. Commun Biol 2020; 3:478. [PMID: 32859965 PMCID: PMC7456325 DOI: 10.1038/s42003-020-01208-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022] Open
Abstract
Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic nematode taxa representing four evolutionary clades (I, III, IV and V). Unlike in C. elegans, 15 species possess multiple (two to five) BCL-2-like proteins, and some do not have any recognisable BCL-2 sequences. Functional studies provided no evidence that BAX/BAK proteins have evolved in nematodes, and structural studies of a BCL-2 protein from the basal clade I revealed it lacks a functionally important feature of the C. elegans orthologue. Clade I CED-4/APAF-1 proteins also possess WD40-repeat sequences associated with apoptosome assembly, not present in C. elegans, or other nematode taxa studied.
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Sci Rep 2020; 10:13775. [PMID: 32792608 PMCID: PMC7426924 DOI: 10.1038/s41598-020-70749-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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38
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Softley CA, Bostock MJ, Popowicz GM, Sattler M. Paramagnetic NMR in drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:287-309. [PMID: 32524233 PMCID: PMC7311382 DOI: 10.1007/s10858-020-00322-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/26/2020] [Indexed: 05/05/2023]
Abstract
The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.
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Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
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Bentley MR, Ilyichova OV, Wang G, Williams ML, Sharma G, Alwan WS, Whitehouse RL, Mohanty B, Scammells PJ, Heras B, Martin JL, Totsika M, Capuano B, Doak BC, Scanlon MJ. Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX). J Med Chem 2020; 63:6863-6875. [DOI: 10.1021/acs.jmedchem.0c00111] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Matthew R. Bentley
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Olga V. Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Martin L. Williams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Gaurav Sharma
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Wesam S. Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Rebecca L. Whitehouse
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Building N75, Brisbane Innovation Park, Don Young Road, Nathan, QLD 4111, Australia
- Vice-Chancellor’s Unit, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Makrina Totsika
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Bradley C. Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Martin J. Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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Sýkorová P, Novotná J, Demo G, Pompidor G, Dubská E, Komárek J, Fujdiarová E, Houser J, Hároníková L, Varrot A, Shilova N, Imberty A, Bovin N, Pokorná M, Wimmerová M. Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed β-propeller fold. Int J Biol Macromol 2020; 152:1113-1124. [DOI: 10.1016/j.ijbiomac.2019.10.200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/08/2023]
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41
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Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. SCIENCE ADVANCES 2020; 6:eaay7919. [PMID: 32284973 PMCID: PMC7124931 DOI: 10.1126/sciadv.aay7919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/08/2020] [Indexed: 06/11/2023]
Abstract
Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.
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Affiliation(s)
- Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Navjeet Ahalawat
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Padmani Sandhu
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Jagannath Mondal
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Millán C, Jiménez E, Schuster A, Diederichs K, Usón I. ALIXE: a phase-combination tool for fragment-based molecular replacement. Acta Crystallogr D Struct Biol 2020; 76:209-220. [PMID: 32133986 PMCID: PMC7057212 DOI: 10.1107/s205979832000056x] [Citation(s) in RCA: 14] [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: 09/18/2019] [Accepted: 01/15/2020] [Indexed: 11/10/2022] Open
Abstract
Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.
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Affiliation(s)
- Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Antonia Schuster
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
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Ding W, Zhang T, He Y, Wang J, Wu L, Han P, Zheng C, Gu Y, Zeng L, Hao Q, Fan H. IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576719015115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.
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Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100018. [PMID: 32647822 PMCID: PMC7337054 DOI: 10.1016/j.yjsbx.2019.100018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 11/23/2022]
Abstract
Thiolases are a well characterized family of enzymes with two distinct categories: degradative, β-ketoadipyl-CoA thiolases and biosynthetic, acetoacetyl-CoA thiolases. Both classes share an identical catalytic triad but catalyze reactions in opposite directions. Moreover, it is established that in contrast to the biosynthetic thiolases the degradative thiolases can accept substrates with broad chain lengths. Hitherto, no residue or structural pattern has been recognized that might help to discern the two thiolases, here we exploit, a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF, as a model system to understand features which distinguishes the two classes using structural studies and bioinformatics analyses. Degradative thiolases have different active site architecture when compared to biosynthetic thiolases, demonstrating the dissimilar chemical nature of the active site architecture. Both thiolases deploy different "anchoring residues" to tether the large Coenzyme A (CoA) or CoA derivatives. Interestingly, the H356 of the catalytic triad in PcaF is directly involved in tethering the CoA/CoA derivatives into the active site and we were able to trap a gridlocked thiolase structure of the H356A mutant, where the CoA was found to be covalently linked to the catalytic cysteine residue, inhibiting the overall reaction. Further, X-ray structures with two long chain CoA derivatives, hexanal-CoA and octanal-CoA helped in delineating the long tunnel of 235 Å2 surface area in PcaF and led to identification of a unique covering loop exclusive to degradative thiolases that plays an active role in determining the tunnel length and the nature of the binding substrate.
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Key Words
- A-mutant-HAL-CoA, A-mutant-hexanal CoA complex
- A-mutant-Hex-CoA, A-mutant-Hexanoyl CoA complex
- A-mutants, H356A Mutant
- AA-mutants, H356A-C386A Mutant
- AS-mutant-OAL-CoA, AS-mutant-octanal CoA complex
- AS-mutant-Oct-CoA, AS-mutant-Octanoyl CoA complex
- AS-mutants, H356A-C90S Mutant
- Covalent locking
- Covering loop
- HAL, hexanal
- Hex-CoA, Hexanoyl CoA
- Hexanoyl CoA
- Mtb-thiolase, Mycobacterium tuberculosis thiolase
- OAL, octanal
- Oct-CoA, Octanoyl CoA
- Octanoyl CoA
- PcaF, β-ketoadipyl-CoA thiolase
- Tunnel
- Zr-thiolase, Zoogleria ramigera thiolase
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45
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The structural bases for agonist diversity in an Arabidopsis thaliana glutamate receptor-like channel. Proc Natl Acad Sci U S A 2019; 117:752-760. [PMID: 31871183 DOI: 10.1073/pnas.1905142117] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Arabidopsis thaliana glutamate receptor-like (GLR) channels are amino acid-gated ion channels involved in physiological processes including wound signaling, stomatal regulation, and pollen tube growth. Here, fluorescence microscopy and genetics were used to confirm the central role of GLR3.3 in the amino acid-elicited cytosolic Ca2+ increase in Arabidopsis seedling roots. To elucidate the binding properties of the receptor, we biochemically reconstituted the GLR3.3 ligand-binding domain (LBD) and analyzed its selectivity profile; our binding experiments revealed the LBD preference for l-Glu but also for sulfur-containing amino acids. Furthermore, we solved the crystal structures of the GLR3.3 LBD in complex with 4 different amino acid ligands, providing a rationale for how the LBD binding site evolved to accommodate diverse amino acids, thus laying the grounds for rational mutagenesis. Last, we inspected the structures of LBDs from nonplant species and generated homology models for other GLR isoforms. Our results establish that GLR3.3 is a receptor endowed with a unique amino acid ligand profile and provide a structural framework for engineering this and other GLR isoforms to investigate their physiology.
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46
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Sharma M, Kumar V. Crystal structure of BinAB toxin receptor (Cqm1) protein and molecular dynamics simulations reveal the role of unique Ca(II) ion. Int J Biol Macromol 2019; 140:1315-1325. [PMID: 31449868 DOI: 10.1016/j.ijbiomac.2019.08.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin that is used world-wide for control of the mosquito population. The protein was crystallized in the presence of a mixture of divalent metal ions. Cqm1 crystal structure was solved using the MRSAD method using Cd(II) anomalous at 1.9 Å wavelength and the structure was refined against 1.8 Å synchrotron data. One tightly bound Ca(II) ion in each of the monomer was observed and this site is suggested here to be unique to the GH13_17 family. Molecular dynamics simulations provide clues for the functional role of Ca(II) ion shown earlier to be essential for enzymatic activity. An optimized substrate (maltotriose) bound structure of the complex was constructed based on which 'retaining-type' mechanism can be predicted reliably. It reveals large conformational change in aromatic residues situated at active-site entrance. A Cd(II) ion was observed overlapping with the substrate-binding site. Kinetics data suggests non-competitive inhibition of Cqm1 by Cd(II). This is the first structure from the GH13_17 family and provides template for constructing reliable models for other members.
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Affiliation(s)
- Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Vinay Kumar
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India.
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Impey RE, Panjikar S, Hall CJ, Bock LJ, Sutton JM, Perugini MA, Soares da Costa TP. Identification of two dihydrodipicolinate synthase isoforms from Pseudomonas aeruginosa that differ in allosteric regulation. FEBS J 2019; 287:386-400. [PMID: 31330085 DOI: 10.1111/febs.15014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/12/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections, accounting for 10% of all hospital-acquired infections. Current antibiotics against P. aeruginosa are becoming increasingly ineffective due to the exponential rise in drug resistance. Thus, there is an urgent need to validate and characterize novel drug targets to guide the development of new classes of antibiotics against this pathogen. One such target is the diaminopimelate (DAP) pathway, which is responsible for the biosynthesis of bacterial cell wall and protein building blocks, namely meso-DAP and lysine. The rate-limiting step of this pathway is catalysed by the enzyme dihydrodipicolinate synthase (DHDPS), typically encoded for in bacteria by a single dapA gene. Here, we show that P. aeruginosa encodes two functional DHDPS enzymes, PaDHDPS1 and PaDHDPS2. Although these isoforms have similar catalytic activities (kcat = 29 s-1 and 44 s-1 for PaDHDPS1 and PaDHDPS2, respectively), they are differentially allosterically regulated by lysine, with only PaDHDPS2 showing inhibition by the end product of the DAP pathway (IC50 = 130 μm). The differences in allostery are attributed to a single amino acid difference in the allosteric binding pocket at position 56. This is the first example of a bacterium that contains multiple bona fide DHDPS enzymes, which differ in allosteric regulation. We speculate that the presence of the two isoforms allows an increase in the metabolic flux through the DAP pathway when required in this clinically important pathogen. DATABASES: PDB ID: 6P90.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lucy J Bock
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - J Mark Sutton
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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48
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Chojnowski G, Pereira J, Lamzin VS. Sequence assignment for low-resolution modelling of protein crystal structures. Acta Crystallogr D Struct Biol 2019; 75:753-763. [PMID: 31373574 PMCID: PMC6677015 DOI: 10.1107/s2059798319009392] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/30/2019] [Indexed: 01/08/2023] Open
Abstract
The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for machine-learning-based docking of main-chain fragments to the sequence and for their sequence-independent connection using a dedicated library of protein fragments. The combined use of these new methods noticeably increases sequence coverage and reduces fragmentation of the protein models automatically built with ARP/wARP.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Truong JQ, Panjikar S, Shearwin-Whyatt L, Bruning JB, Shearwin KE. Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:670-681. [PMID: 31282476 DOI: 10.1107/s2059798319009008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/24/2019] [Indexed: 11/11/2022]
Abstract
Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.
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Affiliation(s)
- Jia Quyen Truong
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Santosh Panjikar
- MX, Australian Synchrotron, 800 Blackburn Road Clayton, Melbourne, VIC 3168, Australia
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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50
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Abstract
The cholesterol-dependent cytolysin (CDC) genes are present in bacterial species that span terrestrial, vertebrate, and invertebrate niches, which suggests that they have evolved to function under widely different environmental conditions. Using a combination of biophysical and crystallographic approaches, we reveal that the relative stability of an intramolecular interface in the archetype CDC perfringolysin O (PFO) plays a central role in regulating its pore-forming properties. The disruption of this interface allows the formation of the membrane spanning β-barrel pore in all CDCs. We show here that the relative strength of the stabilizing forces at this interface directly impacts the energy barrier posed by the transition state for pore formation, as reflected in the Arrhenius activation energy (Ea) for pore formation. This change directly impacts the kinetics and temperature dependence of pore formation. We further show that the interface structure in a CDC from a terrestrial species enables it to function efficiently across a wide range of temperatures by minimizing changes in the strength of the transition state barrier to pore formation. These studies establish a paradigm that CDCs, and possibly other β-barrel pore-forming proteins/toxins, can evolve significantly different pore-forming properties by altering the stability of this transitional interface, which impacts the kinetic parameters and temperature dependence of pore formation.IMPORTANCE The cholesterol-dependent cytolysins (CDCs) are the archetype for the superfamily of oligomeric pore-forming proteins that includes the membrane attack complex/perforin (MACPF) family of immune defense proteins and the stonefish venom toxins (SNTX). The CDC/MACPF/SNTX family exhibits a common protein fold, which forms a membrane-spanning β-barrel pore. We show that changing the relative stability of an extensive intramolecular interface within this fold, which is necessarily disrupted to form the large β-barrel pore, dramatically alters the kinetic and temperature-dependent properties of CDC pore formation. These studies show that the CDCs and other members of the CDC/MACPF/SNTX superfamily have the capacity to significantly alter their pore-forming properties to function under widely different environmental conditions encountered by these species.
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