51
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Jansa J, Jorda R, Škerlová J, Pachl P, Peřina M, Řezníčková E, Heger T, Gucký T, Řezáčová P, Lyčka A, Kryštof V. Imidazo[1,2-c]pyrimidin-5(6H)-one inhibitors of CDK2: Synthesis, kinase inhibition and co-crystal structure. Eur J Med Chem 2021; 216:113309. [PMID: 33711765 DOI: 10.1016/j.ejmech.2021.113309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/15/2022]
Abstract
Pharmacological inhibition of cyclin-dependent kinases has emerged as a possible treatment option for various cancer types. We recently identified substituted imidazo[1,2-c]pyrimidin-5(6H)-ones as inhibitors of cyclin-dependent kinase 2 (CDK2). Here, we report the synthesis of derivatives modified at positions 2, 3, 6 or 8 prepared using Suzuki-Miyaura cross-coupling, halogenation, Dimroth-type rearrangement and alkylation as the main synthetic methods. The compounds displayed micro- to submicromolar inhibition of CDK2/cyclin E activity. Binding of the most potent compound 3b to CDK2 was determined using isothermal titration calorimetry. The co-crystal structure of 3b in complex with fully active CDK2 was solved, revealing the binding mode of 3b in the ATP pocket and a hydrogen bonding interaction with hinge region residue Leu83. Evaluation against leukaemia cell lines revealed low cytotoxicity, which is in line with the high selectivity towards CDK2. This study demonstrates that substituted imidazo[1,2-c]pyrimidines can be exploited for future kinase inhibitor development.
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Affiliation(s)
- Josef Jansa
- Research Institute for Organic Syntheses (VUOS), Rybitví 296, 53354, Pardubice-Rybitví, Czech Republic
| | - Radek Jorda
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Miroslav Peřina
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Eva Řezníčková
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Tomáš Heger
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Tomáš Gucký
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic; Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS), Rybitví 296, 53354, Pardubice-Rybitví, Czech Republic; Faculty of Science, University of Hradec, Rokitanského 62, 50003, Hradec Králové, Czech Republic
| | - Vladimír Kryštof
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic.
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52
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Banerjee A, Goldgur Y, Shuman S. Structure of 3'-PO 4/5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide. RNA (NEW YORK, N.Y.) 2021; 27:rna.078692.121. [PMID: 33619169 PMCID: PMC8051266 DOI: 10.1261/rna.078692.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)-GMP, RNA 3'-phosphate, and RNA3'pp5'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. Here we report a 2.7 Å crystal structure of Pyrococcus horikoshii RtcB in complex with a 6-mer 5'-OH DNA oligonucleotide HOA1pT2pG3pT4pC5pC6, which reveals enzymic contacts of Asn202 to the terminal 5'-OH nucleophile; Arg238 to the A1pT2 and T2pG3 phosphates; Arg190 and Gln194 to the T2pG3 phosphate; and an Arg190 π-cation interaction with the G3 nucleobase. The structural insights affirm functional studies of E. coli RtcB that implicated the conserved counterpart of Arg238 in engagement of the 5'-OH strand for ligation. The essential active site Cys98 that coordinates two manganese ions is oxidized to cysteine sulfonic acid in our structure, raising the prospect that RtcB activity might be sensitive to modulation during oxidative stress.
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53
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Macpherson A, Laabei M, Ahdash Z, Graewert MA, Birtley JR, Schulze MSE, Crennell S, Robinson SA, Holmes B, Oleinikovas V, Nilsson PH, Snowden J, Ellis V, Mollnes TE, Deane CM, Svergun D, Lawson AD, van den Elsen JM. The allosteric modulation of complement C5 by knob domain peptides. eLife 2021; 10:63586. [PMID: 33570492 PMCID: PMC7972453 DOI: 10.7554/elife.63586] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3–6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential. Antibodies are proteins produced by the immune system that can selectively bind to other molecules and modify their behaviour. Cows are highly equipped at fighting-off disease-causing microbes due to the unique shape of some of their antibodies. Unlike other jawed vertebrates, cows’ antibodies contain an ultra-long loop region that contains a ‘knob domain’ which sticks out from the rest of the antibody. Recent research has shown that when detached, the knob domain behaves like an antibody fragment, and can independently bind to a range of different proteins. Antibody fragments are commonly developed in the laboratory to target proteins associated with certain diseases, such as arthritis and cancer. But it was unclear whether the knob domains from cows’ antibodies could also have therapeutic potential. To investigate this, Macpherson et al. studied how knob domains attach to complement C5, a protein in the inflammatory pathway which is a drug target for various diseases, including severe COVID-19. The experiments identified various knob domains that bind to complement C5 and inhibits its activity by altering its structure or movement. Further tests studying the structure of these interactions, led to the discovery of a common mechanism by which inhibitors can modify the behaviour of this inflammatory protein. Complement C5 is involved in numerous molecular pathways in the immune system, which means many of the drugs developed to inhibit its activity can also leave patients vulnerable to infection. However, one of the knob domains identified by Macpherson et al. was found to reduce the activity of complement C5 in some pathways, whilst leaving other pathways intact. This could potentially reduce the risk of bacterial infections which sometimes arise following treatment with these types of inhibitors. These findings highlight a new approach for developing drug inhibitors for complement C5. Furthermore, the ability of knob domains to bind to multiple sites of complement C5 suggests that this fragment could be used to target proteins associated with other diseases.
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Affiliation(s)
- Alex Macpherson
- UCB, Slough, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | | | | | | | - Susan Crennell
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sarah A Robinson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Per H Nilsson
- UCB, Slough, United Kingdom.,Department of Chemistry and Biomedicine, Linnaeus University, Kalmar, Sweden.,Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | | | - Tom Eirik Mollnes
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway.,Research Laboratory, Bodø Hospital, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | - Jean Mh van den Elsen
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
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54
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Sarrou I, Feiler CG, Falke S, Peard N, Yefanov O, Chapman H. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallogr D Struct Biol 2021; 77:224-236. [PMID: 33559611 PMCID: PMC7869899 DOI: 10.1107/s2059798320016071] [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: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.
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Affiliation(s)
- Iosifina Sarrou
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Nolan Peard
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry Chapman
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
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55
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Renner N, Mallery DL, Faysal KMR, Peng W, Jacques DA, Böcking T, James LC. A lysine ring in HIV capsid pores coordinates IP6 to drive mature capsid assembly. PLoS Pathog 2021; 17:e1009164. [PMID: 33524070 PMCID: PMC7850482 DOI: 10.1371/journal.ppat.1009164] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV capsid self-assembles a protective conical shell that simultaneously prevents host sensing whilst permitting the import of nucleotides to drive DNA synthesis. This is accomplished through the construction of dynamic, highly charged pores at the centre of each capsid multimer. The clustering of charges required for dNTP import is strongly destabilising and it is proposed that HIV uses the metabolite IP6 to coordinate the pore during assembly. Here we have investigated the role of inositol phosphates in coordinating a ring of positively charged lysine residues (K25) that forms at the base of the capsid pore. We show that whilst IP5, which can functionally replace IP6, engages an arginine ring (R18) at the top of the pore, the lysine ring simultaneously binds a second IP5 molecule. Dose dependent removal of K25 from the pore severely inhibits HIV infection and concomitantly prevents DNA synthesis. Cryo-tomography reveals that K25A virions have a severe assembly defect that inhibits the formation of mature capsid cones. Monitoring both the kinetics and morphology of capsids assembled in vitro reveals that while mutation K25A can still form tubes, the ability of IP6 to drive assembly of capsid cones has been lost. Finally, in single molecule TIRF microscopy experiments, capsid lattices in permeabilised K25 mutant virions are rapidly lost and cannot be stabilised by IP6. These results suggest that the coordination of IP6 by a second charged ring in mature hexamers drives the assembly of conical capsids capable of reverse transcription and infection.
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Affiliation(s)
- Nadine Renner
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - K. M. Rifat Faysal
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Australia
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Australia
| | - David A. Jacques
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Australia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Australia
| | - Leo C. James
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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56
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Škerlová J, Ismail A, Lindström H, Sjödin B, Mannervik B, Stenmark P. Structural and functional analysis of the inhibition of equine glutathione transferase A3-3 by organotin endocrine disrupting pollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115960. [PMID: 33162212 DOI: 10.1016/j.envpol.2020.115960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/02/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Organotin compounds are highly toxic environmental pollutants with neurotoxic and endocrine-disrupting effects. They are potent inhibitors of glutathione transferases (GSTs), thus impeding their detoxication and antioxidant functions. Several GSTs, including equine GST A3-3 (EcaGST A3-3), exhibit steroid double-bond isomerase activity and are involved in the biosynthesis of testosterone and progesterone. We have performed enzyme kinetics analyses of the inhibition of EcaGST A3-3 by organotin compounds. We have also solved crystal structures of EcaGST A3-3 in complexes with glutathione, and with glutathione together with covalently bound triethyltin. Our structural data indicate that the tin atom forms strong bonds with a covalent character not only with the glutathione, but also with a tyrosyl residue of the enzyme itself, thereby preventing the release of the glutathione-organotin adduct and completely blocking the enzyme function. This work presents a structural basis for the general mechanism of GST inhibition by organotin compounds and contributes to the understanding of their neurotoxic and endocrine disrupting effects.
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Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Aram Ismail
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Helena Lindström
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Bengt Mannervik
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden.
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden; Department of Experimental Medical Science, Lund University, SE-22100, Lund, Sweden.
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57
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Visnes T, Benítez-Buelga C, Cázares-Körner A, Sanjiv K, Hanna BMF, Mortusewicz O, Rajagopal V, Albers JJ, Hagey DW, Bekkhus T, Eshtad S, Baquero JM, Masuyer G, Wallner O, Müller S, Pham T, Göktürk C, Rasti A, Suman S, Torres-Ruiz R, Sarno A, Wiita E, Homan EJ, Karsten S, Marimuthu K, Michel M, Koolmeister T, Scobie M, Loseva O, Almlöf I, Unterlass JE, Pettke A, Boström J, Pandey M, Gad H, Herr P, Jemth AS, El Andaloussi S, Kalderén C, Rodriguez-Perales S, Benítez J, Krokan HE, Altun M, Stenmark P, Berglund UW, Helleday T. Targeting OGG1 arrests cancer cell proliferation by inducing replication stress. Nucleic Acids Res 2020; 48:12234-12251. [PMID: 33211885 PMCID: PMC7708037 DOI: 10.1093/nar/gkaa1048] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022] Open
Abstract
Altered oncogene expression in cancer cells causes loss of redox homeostasis resulting in oxidative DNA damage, e.g. 8-oxoguanine (8-oxoG), repaired by base excision repair (BER). PARP1 coordinates BER and relies on the upstream 8-oxoguanine-DNA glycosylase (OGG1) to recognise and excise 8-oxoG. Here we hypothesize that OGG1 may represent an attractive target to exploit reactive oxygen species (ROS) elevation in cancer. Although OGG1 depletion is well tolerated in non-transformed cells, we report here that OGG1 depletion obstructs A3 T-cell lymphoblastic acute leukemia growth in vitro and in vivo, validating OGG1 as a potential anti-cancer target. In line with this hypothesis, we show that OGG1 inhibitors (OGG1i) target a wide range of cancer cells, with a favourable therapeutic index compared to non-transformed cells. Mechanistically, OGG1i and shRNA depletion cause S-phase DNA damage, replication stress and proliferation arrest or cell death, representing a novel mechanistic approach to target cancer. This study adds OGG1 to the list of BER factors, e.g. PARP1, as potential targets for cancer treatment.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7465 Trondheim,Norway
| | - Carlos Benítez-Buelga
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Varshni Rajagopal
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Julian J Albers
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tove Bekkhus
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Saeed Eshtad
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Juan Miguel Baquero
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation. University of Bath, Bath BA2 7AY, UK
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sarah Müller
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Therese Pham
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Camilla Göktürk
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sharda Suman
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway.,Department of Environment and New Resources, SINTEF Ocean, N-7010 Trondheim, Norway
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Stella Karsten
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Karthick Marimuthu
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Judith Edda Unterlass
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Aleksandra Pettke
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Johan Boström
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Monica Pandey
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Helge Gad
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Patrick Herr
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | | | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Hans E Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway
| | - Mikael Altun
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, SE-221 00 Lund, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
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58
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Songailiene I, Juozapaitis J, Tamulaitiene G, Ruksenaite A, Šulčius S, Sasnauskas G, Venclovas Č, Siksnys V. HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation. Mol Cell 2020; 80:955-970.e7. [PMID: 33290744 DOI: 10.1016/j.molcel.2020.11.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
Prokaryotic toxin-antitoxin (TA) systems are composed of a toxin capable of interfering with key cellular processes and its neutralizing antidote, the antitoxin. Here, we focus on the HEPN-MNT TA system encoded in the vicinity of a subtype I-D CRISPR-Cas system in the cyanobacterium Aphanizomenon flos-aquae. We show that HEPN acts as a toxic RNase, which cleaves off 4 nt from the 3' end in a subset of tRNAs, thereby interfering with translation. Surprisingly, we find that the MNT (minimal nucleotidyltransferase) antitoxin inhibits HEPN RNase through covalent di-AMPylation (diadenylylation) of a conserved tyrosine residue, Y109, in the active site loop. Furthermore, we present crystallographic snapshots of the di-AMPylation reaction at different stages that explain the mechanism of HEPN RNase inactivation. Finally, we propose that the HEPN-MNT system functions as a cellular ATP sensor that monitors ATP homeostasis and, at low ATP levels, releases active HEPN toxin.
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Affiliation(s)
- Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Jonas Juozapaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania.
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59
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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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60
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Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjöström HS, Hilvert D, Baker D, Zeymer C. Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proc Natl Acad Sci U S A 2020; 117:30362-30369. [PMID: 33203677 PMCID: PMC7720202 DOI: 10.1073/pnas.2008535117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
De novo protein design has succeeded in generating a large variety of globular proteins, but the construction of protein scaffolds with cavities that could accommodate large signaling molecules, cofactors, and substrates remains an outstanding challenge. The long, often flexible loops that form such cavities in many natural proteins are difficult to precisely program and thus challenging for computational protein design. Here we describe an alternative approach to this problem. We fused two stable proteins with C2 symmetry-a de novo designed dimeric ferredoxin fold and a de novo designed TIM barrel-such that their symmetry axes are aligned to create scaffolds with large cavities that can serve as binding pockets or enzymatic reaction chambers. The crystal structures of two such designs confirm the presence of a 420 cubic Ångström chamber defined by the top of the designed TIM barrel and the bottom of the ferredoxin dimer. We functionalized the scaffold by installing a metal-binding site consisting of four glutamate residues close to the symmetry axis. The protein binds lanthanide ions with very high affinity as demonstrated by tryptophan-enhanced terbium luminescence. This approach can be extended to other metals and cofactors, making this scaffold a modular platform for the design of binding proteins and biocatalysts.
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Affiliation(s)
- Shane J Caldwell
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Ian C Haydon
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Nikoletta Piperidou
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, Stanford University, Shriram Center for Bioengineering and Chemical Engineering, Stanford, CA 94305
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - H Sebastian Sjöström
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - Cathleen Zeymer
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland;
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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61
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Goh BC, Chua YK, Qian X, Lin J, Savko M, Dedon PC, Lescar J. Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of β-lactam antibiotics. J Struct Biol 2020; 212:107610. [DOI: 10.1016/j.jsb.2020.107610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
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62
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Lia A, Dowle A, Taylor C, Santino A, Roversi P. Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Wellcome Open Res 2020; 5:114. [PMID: 32802964 PMCID: PMC7422855 DOI: 10.12688/wellcomeopenres.15893.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 01/06/2023] Open
Abstract
Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the NAD
+-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate and its reverse reaction in glycolysis and gluconeogenesis. Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase (
HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells. Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein (
HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies of
HsGAPDH across three of the crystal forms obtained is 0.31±0.17. Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result in
HsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.
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Affiliation(s)
- Andrea Lia
- Leicester Institute of Chemical and Structural Biology and Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, LE1 7HB, UK.,Institute of Sciences of Food Production, C.N.R. Unit of Lecce, ia Monteroni, Lecce, 73100, Italy
| | - Adam Dowle
- Bioscience Technology Facility Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Chris Taylor
- Bioscience Technology Facility Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, ia Monteroni, Lecce, 73100, Italy
| | - Pietro Roversi
- Leicester Institute of Chemical and Structural Biology and Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, LE1 7HB, UK
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63
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Hubálek F, Refsgaard HHF, Gram-Nielsen S, Madsen P, Nishimura E, Münzel M, Brand CL, Stidsen CE, Claussen CH, Wulff EM, Pridal L, Ribel U, Kildegaard J, Porsgaard T, Johansson E, Steensgaard DB, Hovgaard L, Glendorf T, Hansen BF, Jensen MK, Nielsen PK, Ludvigsen S, Rugh S, Garibay PW, Moore MC, Cherrington AD, Kjeldsen T. Molecular engineering of safe and efficacious oral basal insulin. Nat Commun 2020; 11:3746. [PMID: 32719315 PMCID: PMC7385171 DOI: 10.1038/s41467-020-17487-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/01/2020] [Indexed: 12/19/2022] Open
Abstract
Recently, the clinical proof of concept for the first ultra-long oral insulin was reported, showing efficacy and safety similar to subcutaneously administered insulin glargine. Here, we report the molecular engineering as well as biological and pharmacological properties of these insulin analogues. Molecules were designed to have ultra-long pharmacokinetic profile to minimize variability in plasma exposure. Elimination plasma half-life of ~20 h in dogs and ~70 h in man is achieved by a strong albumin binding, and by lowering the insulin receptor affinity 500-fold to slow down receptor mediated clearance. These insulin analogues still stimulate efficient glucose disposal in rats, pigs and dogs during constant intravenous infusion and euglycemic clamp conditions. The albumin binding facilitates initial high plasma exposure with a concomitant delay in distribution to peripheral tissues. This slow appearance in the periphery mediates an early transient hepato-centric insulin action and blunts hypoglycaemia in dogs in response to overdosing.
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Affiliation(s)
| | | | | | - Peter Madsen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Erica Nishimura
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Martin Münzel
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | | | | | | | - Erik Max Wulff
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Lone Pridal
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Ulla Ribel
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | | | - Trine Porsgaard
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Eva Johansson
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | | | - Lars Hovgaard
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Tine Glendorf
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Bo Falck Hansen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | | | | | - Svend Ludvigsen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Susanne Rugh
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | | | | | | | - Thomas Kjeldsen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark.
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64
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Shaikhqasem A, Dickmanns A, Neumann P, Ficner R. Characterization of Inhibition Reveals Distinctive Properties for Human and Saccharomyces cerevisiae CRM1. J Med Chem 2020; 63:7545-7558. [PMID: 32585100 DOI: 10.1021/acs.jmedchem.0c00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The receptor CRM1 is responsible for the nuclear export of many tumor-suppressor proteins and viral ribonucleoproteins. This renders CRM1 an interesting target for therapeutic intervention in diverse cancer types and viral diseases. Structural studies of Saccharomyces cerevisiae CRM1 (ScCRM1) complexes with inhibitors defined the molecular basis for CRM1 inhibition. Nevertheless, no structural information is available for inhibitors bound to human CRM1 (HsCRM1). Here, we present the structure of the natural inhibitor Leptomycin B bound to the HsCRM1-RanGTP complex. Despite high sequence conservation and structural similarity in the NES-binding cleft region, ScCRM1 exhibits 16-fold lower binding affinity than HsCRM1 toward PKI-NES and significant differences in affinities toward potential CRM1 inhibitors. In contrast to HsCRM1, competition assays revealed that a human adapted mutant ScCRM1-T539C does not bind all inhibitors tested. Taken together, our data indicate the importance of using HsCRM1 for molecular analysis and development of novel antitumor and antiviral drugs.
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Affiliation(s)
- Alaa Shaikhqasem
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
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65
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Škerlová J, Unterlass J, Göttmann M, Marttila P, Homan E, Helleday T, Jemth AS, Stenmark P. Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. J Biol Chem 2020; 295:11656-11668. [PMID: 32571877 DOI: 10.1074/jbc.ra120.013695] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribonucleotide (CAIR) and l-aspartate to N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). Of note, we present the first structures of human octameric PAICS in complexes with native ligands. In particular, we report the structure of PAICS with CAIR bound in the active sites of both domains and SAICAR bound in one of the SAICAR synthetase domains. Moreover, we report the PAICS structure with SAICAR and an ATP analog occupying the SAICAR synthetase active site. These structures provide insight into substrate and product binding and the architecture of the active sites, disclosing important structural information for rational design of PAICS inhibitors as potential anticancer drugs.
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Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Judith Unterlass
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Mona Göttmann
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden .,Department of Experimental Medical Science, Lund University, Lund, Sweden
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66
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Lia A, Dowle A, Taylor C, Santino A, Roversi P. Partial catalytic Cys oxidation of human GAPDH. Wellcome Open Res 2020; 5:114. [DOI: 10.12688/wellcomeopenres.15893.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the reversible NAD+-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate in both glycolysis and gluconeogenesis.Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase (HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells.Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein (HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies ofHsGAPDH across three of the crystal forms obtained is 0.31±0.17.Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result inHsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.
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67
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Klünemann T, Nimtz M, Jänsch L, Layer G, Blankenfeldt W. Crystal structure of NirF: insights into its role in heme
d
1
biosynthesis. FEBS J 2020; 288:244-261. [DOI: 10.1111/febs.15323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Klünemann
- Structure and Function of Proteins Helmholtz Centre for Infection Research Braunschweig Germany
| | - Manfred Nimtz
- Cellular Proteome Research Helmholtz Centre for Infection Research Braunschweig Germany
| | - Lothar Jänsch
- Cellular Proteome Research Helmholtz Centre for Infection Research Braunschweig Germany
| | - Gunhild Layer
- Institute of Pharmaceutical Sciences Pharmaceutical Biology Albert‐Ludwigs‐Universität Freiburg Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins Helmholtz Centre for Infection Research Braunschweig Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics Technische Universität Braunschweig Germany
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68
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Škerlová J, Lindström H, Gonis E, Sjödin B, Neiers F, Stenmark P, Mannervik B. Structure and steroid isomerase activity of
Drosophila
glutathione transferase E14 essential for ecdysteroid biosynthesis. FEBS Lett 2020; 594:1187-1195. [DOI: 10.1002/1873-3468.13718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/25/2019] [Accepted: 12/11/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Helena Lindström
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Elodie Gonis
- CSGA Laboratory of Taste and Olfaction University Bourgogne Franche‐Comté Dijon France
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Fabrice Neiers
- CSGA Laboratory of Taste and Olfaction University Bourgogne Franche‐Comté Dijon France
| | - Pål Stenmark
- Department of Biochemistry and Biophysics Stockholm University Sweden
- Department of Experimental Medical Science Lund University Sweden
| | - Bengt Mannervik
- Department of Biochemistry and Biophysics Stockholm University Sweden
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69
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A fungal family of lytic polysaccharide monooxygenase-like copper proteins. Nat Chem Biol 2020; 16:345-350. [DOI: 10.1038/s41589-019-0438-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/22/2019] [Indexed: 11/08/2022]
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70
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Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR, Waugh DS. Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res 2019; 47:10134-10150. [PMID: 31199869 DOI: 10.1093/nar/gkz515] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 02/02/2023] Open
Abstract
Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joseph E Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle Needle
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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71
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Mazurkewich S, Poulsen JCN, Lo Leggio L, Larsbrink J. Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components. J Biol Chem 2019; 294:19978-19987. [PMID: 31740581 PMCID: PMC6937553 DOI: 10.1074/jbc.ra119.011435] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Indexed: 12/28/2022] Open
Abstract
Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant resources. However, details on how GEs interact and catalyze degradation of their natural substrates are sparse, calling for thorough enzyme structure-function studies. Presented here is a structural and mechanistic investigation of the bacterial GE OtCE15A. GEs belong to the carbohydrate esterase family 15 (CE15), which is in turn part of the larger α/β-hydrolase superfamily. GEs contain a Ser-His-Asp/Glu catalytic triad, but the location of the catalytic acid in GEs has been shown to be variable, and OtCE15A possesses two putative catalytic acidic residues in the active site. Through site-directed mutagenesis, we demonstrate that these residues are functionally redundant, possibly indicating the evolutionary route toward new functionalities within the family. Structures determined with glucuronate, in both native and covalently bound intermediate states, and galacturonate provide insights into the catalytic mechanism of CE15. A structure of OtCE15A with the glucuronoxylooligosaccharide 23-(4-O-methyl-α-d-glucuronyl)-xylotriose (commonly referred to as XUX) shows that the enzyme can indeed interact with polysaccharides from the plant cell wall, and an additional structure with the disaccharide xylobiose revealed a surface binding site that could possibly indicate a recognition mechanism for long glucuronoxylan chains. Collectively, the results indicate that OtCE15A, and likely most of the CE15 family, can utilize esters of glucuronoxylooligosaccharides and support the proposal that these enzymes work on lignin-carbohydrate complexes in plant biomass.
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Affiliation(s)
- Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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72
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Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2. Nat Commun 2019; 10:4639. [PMID: 31604954 PMCID: PMC6788997 DOI: 10.1038/s41467-019-12614-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/18/2019] [Indexed: 11/25/2022] Open
Abstract
Isocitrate lyase is important for lipid utilisation by Mycobacterium tuberculosis but its ICL2 isoform is poorly understood. Here we report that binding of the lipid metabolites acetyl-CoA or propionyl-CoA to ICL2 induces a striking structural rearrangement, substantially increasing isocitrate lyase and methylisocitrate lyase activities. Thus, ICL2 plays a pivotal role regulating carbon flux between the tricarboxylic acid (TCA) cycle, glyoxylate shunt and methylcitrate cycle at high lipid concentrations, a mechanism essential for bacterial growth and virulence. Isocitrate lyase (ICL) isoforms 1 and 2 are enzymes in the glyoxylate and methylcitrate cycles that enable Mycobacterium tuberculosis (Mtb) to use lipids as a carbon source. Here the authors present the ligand-free Mtb ICL2 and acetyl-CoA bound ICL2 crystal structures, which reveal a structural reorganisation upon acetyl-CoA binding that leads to an activation of its isocitrate lyase and methylcitrate lyase activities.
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73
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Kiss L, Zeng J, Dickson CF, Mallery DL, Yang JC, McLaughlin SH, Boland A, Neuhaus D, James LC. A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases. Nat Commun 2019; 10:4502. [PMID: 31582740 PMCID: PMC6776665 DOI: 10.1038/s41467-019-12388-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosolic antibody receptor TRIM21 possesses unique ubiquitination activity that drives broad-spectrum anti-pathogen targeting and underpins the protein depletion technology Trim-Away. This activity is dependent on formation of self-anchored, K63-linked ubiquitin chains by the heterodimeric E2 enzyme Ube2N/Ube2V2. Here we reveal how TRIM21 facilitates ubiquitin transfer and differentiates this E2 from other closely related enzymes. A tri-ionic motif provides optimally distributed anchor points that allow TRIM21 to wrap an Ube2N~Ub complex around its RING domain, locking the closed conformation and promoting ubiquitin discharge. Mutation of these anchor points inhibits ubiquitination with Ube2N/Ube2V2, viral neutralization and immune signalling. We show that the same mechanism is employed by the anti-HIV restriction factor TRIM5 and identify spatially conserved ionic anchor points in other Ube2N-recruiting RING E3s. The tri-ionic motif is exclusively required for Ube2N but not Ube2D1 activity and provides a generic E2-specific catalysis mechanism for RING E3s.
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Affiliation(s)
- Leo Kiss
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jingwei Zeng
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Claire F Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- University of New South Wales, Sydney, NSW, Australia
| | - Donna L Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Ji-Chun Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Andreas Boland
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - David Neuhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Leo C James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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74
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Frandsen KEH, Tovborg M, Jørgensen CI, Spodsberg N, Rosso MN, Hemsworth GR, Garman EF, Grime GW, Poulsen JCN, Batth TS, Miyauchi S, Lipzen A, Daum C, Grigoriev IV, Johansen KS, Henrissat B, Berrin JG, Lo Leggio L. Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 2019; 294:17117-17130. [PMID: 31471321 DOI: 10.1074/jbc.ra119.009223] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/22/2019] [Indexed: 01/13/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
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Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark.,INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | | | | | | | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Glyn R Hemsworth
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Geoffrey W Grime
- The Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, United Kingdom
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shingo Miyauchi
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, 13009 Marseille, France.,INRA, USC 1408 AFMB, 13009 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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75
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Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site. Sci Rep 2019; 9:12243. [PMID: 31439922 PMCID: PMC6706398 DOI: 10.1038/s41598-019-48579-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/02/2019] [Indexed: 01/15/2023] Open
Abstract
Cholera is a life-threatening diarrhoeal disease caused by the human pathogen Vibrio cholerae. Infection occurs after ingestion of the bacteria, which colonize the human small intestine and secrete their major virulence factor – the cholera toxin (CT). The GM1 ganglioside is considered the primary receptor of the CT, but recent studies suggest that also fucosylated receptors such as histo-blood group antigens are important for cellular uptake and toxicity. Recently, a special focus has been on the histo-blood group antigen Lewisx (Lex), however, where and how the CT binds to Lex remains unclear. Here we report the high-resolution crystal structure (1.5 Å) of the receptor-binding B-subunits of the CT bound to the Lex trisaccharide, and complementary quantitative binding data for CT holotoxins. Lex, and also l-fucose alone, bind to the secondary binding site of the toxin, distinct from the GM1 binding site. In contrast, fucosyl-GM1 mainly binds to the primary binding site due to high-affinity interactions of its GM1 core. Lex is the first histo-blood group antigen of non-secretor phenotype structurally investigated in complex with CT. Together with the quantitative binding data, this allows unique insight into why individuals with non-secretor phenotype are more prone to severe cholera than so-called ‘secretors’.
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76
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Bertinelli M, Paesen GC, Grimes JM, Renner M. High-resolution crystal structure of arthropod Eiger TNF suggests a mode of receptor engagement and altered surface charge within endosomes. Commun Biol 2019; 2:293. [PMID: 31396573 PMCID: PMC6684607 DOI: 10.1038/s42003-019-0541-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
The tumour necrosis factor alpha (TNFα) superfamily of proteins are critical in numerous biological processes, such as in development and immunity. Eiger is the sole TNFα member described in arthropods such as in the important model organism Drosophila. To date there are no structural data on any Eiger protein. Here we present the structure of the TNF domain of Eiger from the fall armyworm Spodoptera frugiperda (SfEiger) to 1.7 Å from a serendipitously obtained crystal without prior knowledge of the protein sequence. Our structure confirms that canonical trimerization is conserved from ancestral TNFs and points towards a mode of receptor engagement. Furthermore, we observe numerous surface histidines on SfEiger, potentially acting as pH switches following internalization into endosomes. Our data contributes to the genome annotation of S. frugiperda, a voracious agricultural pest, and can serve as a basis for future structure-function investigations of the TNF system in related arthropods such as Drosophila.
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Affiliation(s)
- Mattia Bertinelli
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE UK
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
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77
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Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Biochemistry 2019; 58:3144-3154. [PMID: 31260268 PMCID: PMC6791285 DOI: 10.1021/acs.biochem.9b00296] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The c-MYC transcription
factor is a master regulator of cell growth
and proliferation and is an established target for cancer therapy.
This basic helix–loop–helix Zip protein forms a heterodimer
with its obligatory partner MAX, which binds to DNA via the basic
region. Considerable research efforts are focused on targeting the
heterodimerization interface and the interaction of the complex with
DNA. The only available crystal structure is that of a c-MYC:MAX complex
artificially tethered by an engineered disulfide linker and prebound
to DNA. We have carried out a detailed structural analysis of the
apo form of the c-MYC:MAX complex, with no artificial linker, both
in solution using nuclear magnetic resonance (NMR) spectroscopy and
by X-ray crystallography. We have obtained crystal structures in three
different crystal forms, with resolutions between 1.35 and 2.2 Å,
that show extensive helical structure in the basic region. Determination
of the α-helical propensity using NMR chemical shift analysis
shows that the basic region of c-MYC and, to a lesser extent, that
of MAX populate helical conformations. We have also assigned the NMR
spectra of the c-MYC basic helix–loop–helix Zip motif
in the absence of MAX and showed that the basic region has an intrinsic
helical propensity even in the absence of its dimerization partner.
The presence of helical structure in the basic regions in the absence
of DNA suggests that the molecular recognition occurs via a conformational
selection rather than an induced fit. Our work provides both insight
into the mechanism of DNA binding and structural information to aid
in the development of MYC inhibitors.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Fabrice Gorrec
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark D Allen
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
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78
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Devi S, Tarique KF, Ali MF, Abdul Rehman SA, Gourinath S. Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine β-synthase, a distinct member of the PLP-II family. Mol Microbiol 2019; 112:718-739. [PMID: 31132312 DOI: 10.1111/mmi.14315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 02/02/2023]
Abstract
O-acetylserine sulfhydrylase (OASS) and cystathionine β-synthase (CBS) are members of the PLP-II family, and involved in L-cysteine production. OASS produces L-cysteine via a de novo pathway while CBS participates in the reverse transsulfuration pathway. O-acetylserine-dependent CBS (OCBS) was previously identified as a new member of the PLP-II family, which are predominantly seen in bacteria. The bacterium Helicobacter pylori possess only one OASS (hp0107) gene and we showed that the protein coded by this gene actually functions as an OCBS and utilizes L-homocysteine and O-acetylserine (OAS) to produce cystathionine. HpOCBS did not show CBS activity with the substrate L-serine and required OAS exclusively. The HpOCBS structure in complex with methionine showed a closed cleft state, explaining the initial mode of substrate binding. Sequence and structural analyses showed differences between the active sites of OCBS and CBS, and explain their different substrate preferences. We identified three hydrophobic residues near the active site of OCBS, corresponding to one serine and two tyrosine residues in CBSs. Mutational studies were performed on HpOCBS and Saccharomyces cerevisiae CBS. A ScCBS double mutant (Y158F/Y226V) did not display activity with L-serine, indicating indispensability of these polar residues for selecting substrate L-serine, however, did show activity with OAS.
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Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,Public Health Research Institute, Rutgers, Newark, NJ, USA
| | - Mohammad Farhan Ali
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Syed Arif Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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79
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Petronikolou N, Ortega MA, Borisova SA, Nair SK, Metcalf WW. Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin. ACS Chem Biol 2019; 14:742-750. [PMID: 30830751 DOI: 10.1021/acschembio.9b00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Rhizocticins are phosphono-oligopeptide antibiotics that contain a toxic C-terminal ( Z) -l -2-amino-5-phosphono-3-pentenoic acid (APPA) moiety. APPA is an irreversible inhibitor of threonine synthase (ThrC), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of O-phospho-l-homoserine to l-threonine. ThrCs are essential for the viability of bacteria, plants, and fungi and are a target for antibiotic development, as de novo threonine biosynthetic pathway is not found in humans. Given the ability of APPA to interfere in threonine metabolism, it is unclear how the producing strain B. subtilis ATCC 6633 circumvents APPA toxicity. Notably, in addition to the housekeeping APPA-sensitive ThrC ( BsThrC), B. subtilis encodes a second threonine synthase (RhiB) encoded within the rhizocticin biosynthetic gene cluster. Kinetic and spectroscopic analyses show that PLP-dependent RhiB is an authentic threonine synthase, converting O-phospho-l-homoserine to threonine with a catalytic efficiency comparable to BsThrC. To understand the structural basis of inhibition, we determined the crystal structure of APPA bound to the housekeeping BsThrC, revealing a covalent complex between the inhibitor and PLP. Structure-based sequence analyses reveal structural determinants within the RhiB active site that contribute to rendering this ThrC homologue resistant to APPA. Together, this work establishes the self-resistance mechanism utilized by B. subtilis ATCC 6633 against APPA exemplifying one of many ways by which bacteria can overcome phosphonate toxicity.
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Affiliation(s)
- Nektaria Petronikolou
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Manuel A. Ortega
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
| | - Svetlana A. Borisova
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
- Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana Illinois 61801, United States
| | - William W. Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave., Urbana, Illinois 61801, United States
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80
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Ca 2+-dependent regulation of sodium channels Na V1.4 and Na V1.5 is controlled by the post-IQ motif. Nat Commun 2019; 10:1514. [PMID: 30944319 PMCID: PMC6447637 DOI: 10.1038/s41467-019-09570-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/12/2019] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle voltage-gated Na+ channel (NaV1.4) activity is subject to calmodulin (CaM) mediated Ca2+-dependent inactivation; no such inactivation is observed in the cardiac Na+ channel (NaV1.5). Taken together, the crystal structures of the NaV1.4 C-terminal domain relevant complexes and thermodynamic binding data presented here provide a rationale for this isoform difference. A Ca2+-dependent CaM N-lobe binding site previously identified in NaV1.5 is not present in NaV1.4 allowing the N-lobe to signal other regions of the NaV1.4 channel. Consistent with this mechanism, removing this binding site in NaV1.5 unveils robust Ca2+-dependent inactivation in the previously insensitive isoform. These findings suggest that Ca2+-dependent inactivation is effected by CaM's N-lobe binding outside the NaV C-terminal while CaM's C-lobe remains bound to the NaV C-terminal. As the N-lobe binding motif of NaV1.5 is a mutational hotspot for inherited arrhythmias, the contributions of mutation-induced changes in CDI to arrhythmia generation is an intriguing possibility.
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81
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Visnes T, Cázares-Körner A, Hao W, Wallner O, Masuyer G, Loseva O, Mortusewicz O, Wiita E, Sarno A, Manoilov A, Astorga-Wells J, Jemth AS, Pan L, Sanjiv K, Karsten S, Gokturk C, Grube M, Homan EJ, Hanna BMF, Paulin CBJ, Pham T, Rasti A, Berglund UW, von Nicolai C, Benitez-Buelga C, Koolmeister T, Ivanic D, Iliev P, Scobie M, Krokan HE, Baranczewski P, Artursson P, Altun M, Jensen AJ, Kalderén C, Ba X, Zubarev RA, Stenmark P, Boldogh I, Helleday T. Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation. Science 2019; 362:834-839. [PMID: 30442810 DOI: 10.1126/science.aar8048] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/30/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1-deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-α-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor κB and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7465 Trondheim, Norway
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Wenjing Hao
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research, and Innovation in Central Norway, Trondheim, Norway
| | - Aleksandr Manoilov
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Lang Pan
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Stella Karsten
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Camilla Gokturk
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Maurice Grube
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Therese Pham
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Catharina von Nicolai
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Dag Ivanic
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Petar Iliev
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Hans E Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research, and Innovation in Central Norway, Trondheim, Norway
| | - Pawel Baranczewski
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Science for Life Laboratory Drug Discovery and Development Platform, ADME of Therapeutics Facility, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Uppsala Drug Optimisation and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Science for Life Laboratory Drug Discovery and Development Platform, ADME of Therapeutics Facility, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Uppsala Drug Optimisation and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Mikael Altun
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Annika Jenmalm Jensen
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Xueqing Ba
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden.,Department of Pharmacological and Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Istvan Boldogh
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden. .,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
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82
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Bonnardel F, Kumar A, Wimmerova M, Lahmann M, Perez S, Varrot A, Lisacek F, Imberty A. Architecture and Evolution of Blade Assembly in β-propeller Lectins. Structure 2019; 27:764-775.e3. [PMID: 30853410 DOI: 10.1016/j.str.2019.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/10/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022]
Abstract
Lectins with a β-propeller fold bind glycans on the cell surface through multivalent binding sites and appropriate directionality. These proteins are formed by repeats of short domains, raising questions about evolutionary duplication. However, these repeats are difficult to detect in translated genomes and seldom correctly annotated in sequence databases. To address these issues, we defined the blade signature of the five types of β-propellers using 3D-structural data. With these templates, we predicted 3,887 β-propeller lectins in 1,889 species and organized this information in a searchable online database. The data reveal a widespread distribution of β-propeller lectins across species. Prediction also emphasizes multiple architectures and led to the discovery of a β-propeller assembly scenario. This was confirmed by producing and characterizing a predicted protein coded in the genome of Kordia zhangzhouensis. The crystal structure uncovers an intermediate in the evolution of β-propeller assembly and demonstrates the power of our tools.
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Affiliation(s)
- François Bonnardel
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France; Swiss Institute of Bioinformatics, 1227 Geneva, Switzerland; Computer Science Department, UniGe, 1227 Geneva, Switzerland
| | - Atul Kumar
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France; CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Michaela Wimmerova
- CEITEC, Masaryk University, 625 00 Brno, Czech Republic; NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Martina Lahmann
- School of Chemistry, University of Bangor, LL57 2UW Bangor, UK
| | - Serge Perez
- University of Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Annabelle Varrot
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, 1227 Geneva, Switzerland; Computer Science Department, UniGe, 1227 Geneva, Switzerland; Section of Biology, UniGe, 1205 Geneva, Switzerland.
| | - Anne Imberty
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
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83
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Arnling Bååth J, Mazurkewich S, Poulsen JCN, Olsson L, Lo Leggio L, Larsbrink J. Structure-function analyses reveal that a glucuronoyl esterase from Teredinibacter turnerae interacts with carbohydrates and aromatic compounds. J Biol Chem 2019; 294:6635-6644. [PMID: 30814248 PMCID: PMC6484129 DOI: 10.1074/jbc.ra119.007831] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/20/2019] [Indexed: 11/06/2022] Open
Abstract
Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages found between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant resources. However, details on how GEs interact with their natural substrates are sparse, calling for thorough structure-function studies. Presented here is the structure and biochemical characterization of a GE, TtCE15A, from the bacterium Teredinibacter turnerae, a symbiont of wood-boring shipworms. To gain deeper insight into enzyme-substrate interactions, inhibition studies were performed with both the WT TtCE15A and variants in which we, by using site-directed mutagenesis, substituted residues suggested to have key roles in binding to or interacting with the aromatic and carbohydrate structures of its uronic acid ester substrates. Our results support the hypothesis that two aromatic residues (Phe-174 and Trp-376), conserved in bacterial GEs, interact with aromatic and carbohydrate structures of these substrates in the enzyme active site, respectively. The solved crystal structure of TtCE15A revealed features previously not observed in either fungal or bacterial GEs, with a large inserted N-terminal region neighboring the active site and a differently positioned residue of the catalytic triad. The findings highlight key interactions between GEs and complex lignin-carbohydrate ester substrates and advance our understanding of the substrate specificities of these enzymes in biomass conversion.
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Affiliation(s)
- Jenny Arnling Bååth
- From the Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden and
| | - Scott Mazurkewich
- From the Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden and
| | | | - Lisbeth Olsson
- From the Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden and
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- From the Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden and
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84
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Jones HG, Wrapp D, Gilman MSA, Battles MB, Wang N, Sacerdote S, Chuang GY, Kwong PD, McLellan JS. Iterative screen optimization maximizes the efficiency of macromolecular crystallization. Acta Crystallogr F Struct Biol Commun 2019; 75:123-131. [PMID: 30713164 PMCID: PMC6360444 DOI: 10.1107/s2053230x18017338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 11/11/2022] Open
Abstract
Advances in X-ray crystallography have streamlined the process of determining high-resolution three-dimensional macromolecular structures. However, a rate-limiting step in this process continues to be the generation of crystals that are of sufficient size and quality for subsequent diffraction experiments. Here, iterative screen optimization (ISO), a highly automated process in which the precipitant concentrations of each condition in a crystallization screen are modified based on the results of a prior crystallization experiment, is described. After designing a novel high-throughput crystallization screen to take full advantage of this method, the value of ISO is demonstrated by using it to successfully crystallize a panel of six diverse proteins. The results suggest that ISO is an effective method to obtain macromolecular crystals, particularly for proteins that crystallize under a narrow range of precipitant concentrations.
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Affiliation(s)
- Harrison G. Jones
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Daniel Wrapp
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Morgan S. A. Gilman
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Michael B. Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Nianshuang Wang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Sofia Sacerdote
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason S. McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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85
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Sabaratnam K, Renner M, Paesen G, Harlos K, Nair V, Owens RJ, Grimes JM. Insights from the crystal structure of the chicken CREB3 bZIP suggest that members of the CREB3 subfamily transcription factors may be activated in response to oxidative stress. Protein Sci 2019; 28:779-787. [PMID: 30653278 PMCID: PMC6423718 DOI: 10.1002/pro.3573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/14/2019] [Indexed: 12/23/2022]
Abstract
cAMP response element binding Protein 3 (CREB3) is an endoplasmic reticulum (ER) membrane‐bound transcription factor, which belongs to the basic leucine zipper (bZIP) superfamily of eukaryotic transcription factors. CREB3 plays a role in the ER‐stress induced unfolded protein response (UPR) and is a multifunctional cellular factor implicated in a number of biological processes including cell proliferation and migration, tumor suppression, and immune‐related gene expression. To gain structural insights into the transcription factor, we determined the crystal structure of the conserved bZIP domain of chicken CREB3 (chCREB3) to a resolution of 3.95 Å. The X‐ray structure provides evidence that chCREB3 can form a stable homodimer. The chCREB3 bZIP has a structured, pre‐formed DNA binding region, even in the absence of DNA, a feature that could potentially enhance both the DNA binding specificity and affinity of chCREB3. Significantly, the homodimeric bZIP possesses an intermolecular disulfide bond that connects equivalent cysteine residues of the parallel helices in the leucine zipper region. This disulfide bond in the hydrophobic core of the bZIP may increase the stability of the homodimer under oxidizing conditions. Moreover, sequence alignment of bZIP sequences from chicken, human, and mouse reveals that only members of the CREB3 subfamily contain this cysteine residue, indicating that it could act as a redox‐sensor. Taken together, these results suggest that the activity of these transcription factors may be redox‐regulated and they may be activated in response to oxidative stress. PDB Code(s): 6IAK
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Affiliation(s)
- Keshalini Sabaratnam
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,The Pirbright Institute, Woking, Guildford, Surrey, GU24 0NF, United Kingdom
| | - Max Renner
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Guido Paesen
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Woking, Guildford, Surrey, GU24 0NF, United Kingdom
| | - Raymond J Owens
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,The Research Complex at Harwell, Oxfordshire, OX11 0FA, United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,Diamond Light Source Limited, Oxfordshire, OX11 0DE, United Kingdom
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86
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Sekula B, Dauter Z. Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:555. [PMID: 31134111 PMCID: PMC6514230 DOI: 10.3389/fpls.2019.00555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/11/2019] [Indexed: 05/14/2023]
Abstract
Spermidine synthases (SPDSs) catalyze the production of the linear triamine, spermidine, from putrescine. They utilize decarboxylated S-adenosylmethionine (dc-SAM), a universal cofactor of aminopropyltransferases, as a donor of the aminopropyl moiety. In this work, we describe crystal structures of two SPDS isoforms from Arabidopsis thaliana (AtSPDS1 and AtSPDS2). AtSPDS1 and AtSPDS2 are dimeric enzymes that share the fold of the polyamine biosynthesis proteins. Subunits of both isoforms present the characteristic two-domain structure. Smaller, N-terminal domain is built of the two β-sheets, while the C-terminal domain has a Rossmann fold-like topology. The catalytic cleft composed of two main compartments, the dc-SAM binding site and the polyamine groove, is created independently in each AtSPDS subunits at the domain interface. We also provide the structural details about the dc-SAM binding mode and the inhibition of SPDS by a potent competitive inhibitor, cyclohexylamine (CHA). CHA occupies the polyamine binding site of AtSPDS where it is bound at the bottom of the active site with the amine group placed analogously to the substrate. The crystallographic snapshots show in detail the structural rearrangements of AtSPDS1 and AtSPDS2 that are required to stabilize ligands within the active site. The concerted movements are observed in both compartments of the catalytic cleft, where three major parts significantly change their conformation. These are (i) the neighborhood of the glycine-rich region where aminopropyl moiety of dc-SAM is bound, (ii) the very flexible gate region with helix η6, which interacts with both, the adenine moiety of dc-SAM and the bound polyamine or inhibitor, and (iii) the N-terminal β-hairpin, that limits the putrescine binding grove at the bottom of the catalytic site.
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87
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Salimraj R, Hinchliffe P, Kosmopoulou M, Tyrrell JM, Brem J, van Berkel SS, Verma A, Owens RJ, McDonough MA, Walsh TR, Schofield CJ, Spencer J. Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases. FEBS J 2019; 286:169-183. [PMID: 30430727 PMCID: PMC6326847 DOI: 10.1111/febs.14695] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/06/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
Metallo-β-Lactamases (MBLs) protect bacteria from almost all β-lactam antibiotics. Verona integron-encoded MBL (VIM) enzymes are among the most clinically important MBLs, with VIM-1 increasing in carbapenem-resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are among the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here, we present crystal structures of VIM-1 and its complexes with a substrate-mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM-1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water-mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221-bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs. ENZYMES: EC 3.5.2.6 DATABASES: Co-ordinates and structure factors for protein structures described in this manuscript have been deposited in the Protein Data Bank (www.rcsb.org/pdb) with accession codes 5N5G (VIM-1), 5N5H (VIM-1:ML302F complex) and 5N5I (VIM-1-hydrolysed meropenem complex).
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | | | | | | | - Jürgen Brem
- Department of ChemistryUniversity of OxfordUK
| | | | - Anil Verma
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | - Raymond J. Owens
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | | | | | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of BristolUK
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88
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Pinheiro J, Biboy J, Vollmer W, Hirt RP, Keown JR, Artuyants A, Black MM, Goldstone DC, Simoes-Barbosa A. The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases. mBio 2018; 9:e01784-18. [PMID: 30538181 PMCID: PMC6299479 DOI: 10.1128/mbio.01784-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 02/01/2023] Open
Abstract
The human eukaryotic pathogen Trichomonas vaginalis causes trichomoniasis, a prevalent sexually transmitted infection. This extracellular protozoan is intimately associated with the human vaginal mucosa and microbiota, but key aspects of the complex interactions between the parasite and the vaginal bacteria remain elusive. We report that T. vaginalis has acquired, by lateral gene transfer from bacteria, genes encoding peptidoglycan hydrolases of the NlpC/P60 family. Two of the T. vaginalis enzymes were active against bacterial peptidoglycan, retaining the active-site fold and specificity as dl-endopeptidases. The endogenous NlpC/P60 genes are transcriptionally upregulated in T. vaginalis in the presence of bacteria. The overexpression of an exogenous copy enables the parasite to outcompete bacteria from mixed cultures, consistent with the biochemical activity of the enzyme. Our study results highlight the relevance of the interactions of this eukaryotic pathogen with bacteria, a poorly understood aspect of the biology of this important human parasite.IMPORTANCETrichomonas vaginalis is a parasitic protozoan of the human urogenital tract that causes trichomoniasis, a very common sexually transmitted disease. Despite residing extracellularly and in close association with the vaginal bacteria (i.e., the microbiota), very little is known about the nature of the parasite-bacterium interactions. Our study showed that this parasite had acquired genes from bacteria which retained their original function. They produce active enzymes capable of degrading peptidoglycan, a unique polymer of the bacterial cell envelope, helping the parasite to outcompete bacteria in mixed cultures. This study was the first to show that a laterally acquired group of genes enables a eukaryotic mucosal pathogen to control bacterial population. We highlight the importance of understanding the interactions between pathogens and microbiota, as the outcomes of these interactions are increasingly understood to have important implications on health and disease.
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Affiliation(s)
- Jully Pinheiro
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeremy R Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Moyra M Black
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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89
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Sievers QL, Petzold G, Bunker RD, Renneville A, Słabicki M, Liddicoat BJ, Abdulrahman W, Mikkelsen T, Ebert BL, Thomä NH. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science 2018; 362:eaat0572. [PMID: 30385546 PMCID: PMC6326779 DOI: 10.1126/science.aat0572] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/28/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys2-His2 (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4CRBN E3 ubiquitin ligase. We screened the human C2H2 zinc finger proteome for degradation in the presence of thalidomide analogs, identifying 11 zinc finger degrons. Structural and functional characterization of the C2H2 zinc finger degrons demonstrates how diverse zinc finger domains bind the permissive drug-CRBN interface. Computational zinc finger docking and biochemical analysis predict that more than 150 zinc fingers bind the drug-CRBN complex in vitro, and we show that selective zinc finger degradation can be achieved through compound modifications. Our results provide a rationale for therapeutically targeting transcription factors that were previously considered undruggable.
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Affiliation(s)
- Quinlan L Sievers
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Brigham and Women's Hospital, Division of Hematology, Harvard Medical School, Boston, MA 02115, USA
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aline Renneville
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Brigham and Women's Hospital, Division of Hematology, Harvard Medical School, Boston, MA 02115, USA
| | - Mikołaj Słabicki
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Brigham and Women's Hospital, Division of Hematology, Harvard Medical School, Boston, MA 02115, USA
- Division of Translational Oncology, National Center for Tumor Diseases, Heidelberg and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Brian J Liddicoat
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Brigham and Women's Hospital, Division of Hematology, Harvard Medical School, Boston, MA 02115, USA
| | - Wassim Abdulrahman
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Benjamin L Ebert
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
- Brigham and Women's Hospital, Division of Hematology, Harvard Medical School, Boston, MA 02115, USA
- Dana Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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90
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Abstract
There are several options available for intravenous application of iron supplements, but they all have a similar structure:—an iron core surrounded by a carbohydrate coating. These nanoparticles require processing by the reticuloendothelial system to release iron, which is subsequently picked up by the iron-binding protein transferrin and distributed throughout the body, with most of the iron supplied to the bone marrow. This process risks exposing cells and tissues to free iron, which is potentially toxic due to its high redox activity. A new parenteral iron formation, ferric pyrophosphate citrate (FPC), has a novel structure that differs from conventional intravenous iron formulations, consisting of an iron atom complexed to one pyrophosphate and two citrate anions. In this study, we show that FPC can directly transfer iron to apo-transferrin. Kinetic analyses reveal that FPC donates iron to apo-transferrin with fast binding kinetics. In addition, the crystal structure of transferrin bound to FPC shows that FPC can donate iron to both iron-binding sites found within the transferrin structure. Examination of the iron-binding sites demonstrates that the iron atoms in both sites are fully encapsulated, forming bonds with amino acid side chains in the protein as well as pyrophosphate and carbonate anions. Taken together, these data demonstrate that, unlike intravenous iron formulations, FPC can directly and rapidly donate iron to transferrin in a manner that does not expose cells and tissues to the damaging effects of free, redox-active iron.
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91
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Plavša JJ, Řezáčová P, Kugler M, Pachl P, Brynda J, Voburka Z, Ćelić A, Petri ET, Škerlová J. In situ proteolysis of an N-terminal His tag with thrombin improves the diffraction quality of human aldo-keto reductase 1C3 crystals. Acta Crystallogr F Struct Biol Commun 2018; 74:300-306. [PMID: 29717998 PMCID: PMC5931143 DOI: 10.1107/s2053230x18005721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/12/2018] [Indexed: 11/11/2022] Open
Abstract
Human aldo-keto reductase 1C3 (AKR1C3) stereospecifically reduces steroids and prostaglandins and is involved in the biotransformation of xenobiotics. Its role in various cancers makes it a potential therapeutic target for the development of inhibitors. Recombinant AKR1C3 with a thrombin-cleavable N-terminal His6 tag was expressed from a pET-28(+) vector for structural studies of enzyme-inhibitor complexes. A modified in situ proteolysis approach was applied to specifically remove the His tag by thrombin cleavage during crystallization screening trials. This improved the morphology and diffraction quality of the crystals and allowed the acquisition of high-resolution diffraction data and structure solution. This approach may be generally applicable to other proteins expressed using the pET-28(+) vector.
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Affiliation(s)
- Jovana J. Plavša
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Zdeněk Voburka
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Anđelka Ćelić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Edward T. Petri
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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92
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Guo J, Coker AR, Wood SP, Cooper JB, Keegan RM, Ahmad N, Muhammad MA, Rashid N, Akhtar M. Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:305-314. [PMID: 29652257 DOI: 10.1107/s2059798318001754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022]
Abstract
Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100°C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Alun R Coker
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Steve P Wood
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Jonathan B Cooper
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Ronan M Keegan
- CCP4, Research Complex at Harwell and Science and Technology Facilities Council, Rutherford Appleton Laboratories, Harwell Oxford, Didcot OX11 0FA, England
| | - Nasir Ahmad
- Institute of Agricultural Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhummad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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93
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Dickmanns A, Zschiedrich CP, Arens J, Parfentev I, Gundlach J, Hofele R, Neumann P, Urlaub H, Görke B, Ficner R, Stülke J. Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh in Bacillus subtilis. J Biol Chem 2018. [PMID: 29514981 DOI: 10.1074/jbc.ra117.001289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Utilization of energy-rich carbon sources such as glucose is fundamental to the evolutionary success of bacteria. Glucose can be catabolized via glycolysis for feeding the intermediary metabolism. The methylglyoxal synthase MgsA produces methylglyoxal from the glycolytic intermediate dihydroxyacetone phosphate. Methylglyoxal is toxic, requiring stringent regulation of MgsA activity. In the Gram-positive bacterium Bacillus subtilis, an interaction with the phosphoprotein Crh controls MgsA activity. In the absence of preferred carbon sources, Crh is present in the nonphosphorylated state and binds to and thereby inhibits MgsA. To better understand the mechanism of regulation of MgsA, here we performed biochemical and structural analyses of B. subtilis MgsA and of its interaction with Crh. Our results indicated that MgsA forms a hexamer (i.e. a trimer of dimers) in the crystal structure, whereas it seems to exist in an equilibrium between a dimer and hexamer in solution. In the hexamer, two alternative dimers could be distinguished, but only one appeared to prevail in solution. Further analysis strongly suggested that the hexamer is the biologically active form. In vitro cross-linking studies revealed that Crh interacts with the N-terminal helices of MgsA and that the Crh-MgsA binding inactivates MgsA by distorting and thereby blocking its active site. In summary, our results indicate that dimeric and hexameric MgsA species exist in an equilibrium in solution, that the hexameric species is the active form, and that binding to Crh deforms and blocks the active site in MgsA.
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Affiliation(s)
| | | | - Johannes Arens
- From the Departments of Molecular Structural Biology and
| | - Iwan Parfentev
- the Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and.,the Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jan Gundlach
- General Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Romina Hofele
- the Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and.,the Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Piotr Neumann
- From the Departments of Molecular Structural Biology and
| | - Henning Urlaub
- the Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and.,the Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Boris Görke
- General Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ralf Ficner
- From the Departments of Molecular Structural Biology and
| | - Jörg Stülke
- General Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany,
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94
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Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS). CRYSTALS 2018. [DOI: 10.3390/cryst8030109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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95
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Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms. Nat Commun 2018; 9:651. [PMID: 29440755 PMCID: PMC5811534 DOI: 10.1038/s41467-018-03045-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
Missense mutations in MORC2 cause neuropathies including spinal muscular atrophy and Charcot-Marie-Tooth disease. We recently identified MORC2 as an effector of epigenetic silencing by the human silencing hub (HUSH). Here we report the biochemical and cellular activities of MORC2 variants, alongside crystal structures of wild-type and neuropathic forms of a human MORC2 fragment comprising the GHKL-type ATPase module and CW-type zinc finger. This fragment dimerizes upon binding ATP and contains a hinged, functionally critical coiled-coil insertion absent in other GHKL ATPases. We find that dimerization and DNA binding of the MORC2 ATPase module transduce HUSH-dependent silencing. Disease mutations change the dynamics of dimerization by distinct structural mechanisms: destabilizing the ATPase-CW module, trapping the ATP lid, or perturbing the dimer interface. These defects lead to the modulation of HUSH function, thus providing a molecular basis for understanding MORC2-associated neuropathies.
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96
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Yewdall NA, Peskin AV, Hampton MB, Goldstone DC, Pearce FG, Gerrard JA. Quaternary structure influences the peroxidase activity of peroxiredoxin 3. Biochem Biophys Res Commun 2018; 497:558-563. [PMID: 29438714 DOI: 10.1016/j.bbrc.2018.02.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/09/2018] [Indexed: 12/16/2022]
Abstract
Peroxiredoxins are abundant peroxidase enzymes that are key regulators of the cellular redox environment. A major subgroup of these proteins, the typical 2-Cys peroxiredoxins, can switch between dimers and decameric or dodecameric rings, during the catalytic cycle. The necessity of this change in quaternary structure for function as a peroxidase is not fully understood. In order to explore this, human peroxiredoxin 3 (Prx3) protein was engineered to form both obligate dimers (S75E Prx3) and stabilised dodecameric rings (S78C Prx3), uncoupling structural transformations from the catalytic cycle. The obligate dimer, S75E Prx3, retained catalytic activity towards hydrogen peroxide, albeit significantly lower than the wildtype and S78C proteins, suggesting an evolutionary advantage of having higher order self-assemblies.
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Affiliation(s)
- N Amy Yewdall
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington 6140, New Zealand; School of Chemical Sciences, University of Auckland, Auckland 1010, New Zealand.
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97
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Gu A, Marshall B, Rosa N, Ristic M, Newman J. Organizing a crystallization laboratory. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576717016727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
Managing chemical stocks and samples in any laboratory is an arduous task; in a crystallization laboratory this is particularly burdensome, given the need for many stocks to facilitate optimization of crystal hits obtained from screening experiments. Although inventory management is widespread in retail and other arenas, most small academic laboratories do not adopt formal stock management systems. Without an overarching system for handling stocks and samples, problems such as stock duplication, inappropriate stock storage and insufficient labelling are rife. Two applications have been developed in the Collaborative Crystallization Centre, the first of which manages the hundreds of stocks used for crystallization, and a second which manages protein (and other) samples stored in the 193 K freezer. Both applications are built around a simple database, with a Python front end that allows samples or stocks to be scanned in or out. Information from a decade of crystallization stock usage allows a good estimation of what chemicals are used (and in what quantities) in a crystallization laboratory.
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98
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Ting YT, Petersen J, Ramarathinam SH, Scally SW, Loh KL, Thomas R, Suri A, Baker DG, Purcell AW, Reid HH, Rossjohn J. The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis. J Biol Chem 2018; 293:3236-3251. [PMID: 29317506 DOI: 10.1074/jbc.ra117.001013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/21/2017] [Indexed: 12/22/2022] Open
Abstract
The HLA-DRB1 locus is strongly associated with rheumatoid arthritis (RA) susceptibility, whereupon citrullinated self-peptides bind to HLA-DR molecules bearing the shared epitope (SE) amino acid motif. However, the differing propensity for citrullinated/non-citrullinated self-peptides to bind given HLA-DR allomorphs remains unclear. Here, we used a fluorescence polarization assay to determine a hierarchy of binding affinities of 34 self-peptides implicated in RA against three HLA-DRB1 allomorphs (HLA-DRB1*04:01/*04:04/*04:05) each possessing the SE motif. For all three HLA-DRB1 allomorphs, we observed a strong correlation between binding affinity and citrullination at P4 of the bound peptide ligand. A differing hierarchy of peptide-binding affinities across the three HLA-DRB1 allomorphs was attributable to the β-chain polymorphisms that resided outside the SE motif and were consistent with sequences of naturally presented peptide ligands. Structural determination of eight HLA-DR4-self-epitope complexes revealed strict conformational convergence of the P4-Cit and surrounding HLA β-chain residues. Polymorphic residues that form part of the P1 and P9 pockets of the HLA-DR molecules provided a structural basis for the preferential binding of the citrullinated self-peptides to the HLA-DR4 allomorphs. Collectively, we provide a molecular basis for the interplay between citrullination of self-antigens and HLA polymorphisms that shape peptide-HLA-DR4 binding affinities in RA.
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Affiliation(s)
- Yi Tian Ting
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Jan Petersen
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Sri H Ramarathinam
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Stephen W Scally
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Khai L Loh
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Ranjeny Thomas
- the University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Anish Suri
- the Janssen Research and Development, Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, B-2340-Beerse, Belgium
| | - Daniel G Baker
- the Janssen Research and Development, LLC, Spring House, Pennsylvania 19002, and
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Hugh H Reid
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
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99
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Zhou RB, Lu XL, Dong C, Ahmad F, Zhang CY, Yin DC. Application of protein crystallization methodologies to enhance the solubility, stability and monodispersity of proteins. CrystEngComm 2018. [DOI: 10.1039/c7ce02189e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Application of protein crystallization methodologies to screen optimal solution formulations for proteins prone to aggregation.
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Affiliation(s)
- Ren-Bin Zhou
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Xiao-Li Lu
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Chen Dong
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Fiaz Ahmad
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Chen-Yan Zhang
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
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100
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Arnling Bååth J, Mazurkewich S, Knudsen RM, Poulsen JCN, Olsson L, Lo Leggio L, Larsbrink J. Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:213. [PMID: 30083226 PMCID: PMC6069808 DOI: 10.1186/s13068-018-1213-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/23/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration. RESULTS Ten CE15 enzymes from three bacterial species, sharing as little as 20% sequence identity, were characterized on a range of model substrates; two protein structures were solved, and insights into their regulation and biological roles were gained through gene expression analysis and enzymatic assays on complex biomass. Several enzymes with higher catalytic efficiencies on a wider range of model substrates than previously characterized fungal GEs were identified. Similarities and differences regarding substrate specificity between the investigated GEs were observed and putatively linked to their positioning in the CE15 phylogenetic tree. The bacterial GEs were able to utilize substrates lacking 4-OH methyl substitutions, known to be important for fungal enzymes. In addition, certain bacterial GEs were able to efficiently cleave esters of galacturonate, a functionality not previously described within the family. The two solved structures revealed similar overall folds to known structures, but also indicated active site regions allowing for more promiscuous substrate specificities. The gene expression analysis demonstrated that bacterial GE-encoding genes were differentially expressed as response to different carbon sources. Further, improved enzymatic saccharification of milled corn cob by a commercial lignocellulolytic enzyme cocktail when supplemented with GEs showcased their synergistic potential with other enzyme types on native biomass. CONCLUSIONS Bacterial GEs exhibit much larger diversity than fungal counterparts. In this study, we significantly expanded the existing knowledge on CE15 with the in-depth characterization of ten bacterial GEs broadly spanning the phylogenetic tree, and also presented two novel enzyme structures. Variations in transcriptional responses of CE15-encoding genes under different growth conditions suggest nonredundant functions for enzymes found in species with multiple CE15 genes and further illuminate the importance of GEs in native lignin-carbohydrate disassembly.
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Affiliation(s)
- Jenny Arnling Bååth
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Lisbeth Olsson
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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