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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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2
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Banerjee S, Varga JK, Kumar M, Zoltsman G, Rotem-Bamberger S, Cohen-Kfir E, Isupov MN, Rosenzweig R, Schueler-Furman O, Wiener R. Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation. EMBO Rep 2023; 24:e56920. [PMID: 37988244 DOI: 10.15252/embr.202356920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023] Open
Abstract
Ufmylation plays a crucial role in various cellular processes including DNA damage response, protein translation, and ER homeostasis. To date, little is known about how the enzymes responsible for ufmylation coordinate their action. Here, we study the details of UFL1 (E3) activity, its binding to UFC1 (E2), and its relation to UBA5 (E1), using a combination of structural modeling, X-ray crystallography, NMR, and biochemical assays. Guided by Alphafold2 models, we generate an active UFL1 fusion construct that includes its partner DDRGK1 and solve the crystal structure of this critical interaction. This fusion construct also unveiled the importance of the UFL1 N-terminal helix for binding to UFC1. The binding site suggested by our UFL1-UFC1 model reveals a conserved interface, and competition between UFL1 and UBA5 for binding to UFC1. This competition changes in the favor of UFL1 following UFM1 charging of UFC1. Altogether, our study reveals a novel, terminal helix-mediated regulatory mechanism, which coordinates the cascade of E1-E2-E3-mediated transfer of UFM1 to its substrate and provides new leads to target this modification.
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Affiliation(s)
- Sayanika Banerjee
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Julia K Varga
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manoj Kumar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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3
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De Rose SA, Isupov MN, Worthy HL, Stracke C, Harmer NJ, Siebers B, Littlechild JA. Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus. Front Microbiol 2023; 14:1267570. [PMID: 38045033 PMCID: PMC10690619 DOI: 10.3389/fmicb.2023.1267570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 12/05/2023] Open
Abstract
The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as Methanothermus fervidus, Methanopyrus kandleri, and Methanothermobacter thermoautotrophicus. Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent SN2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.
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Affiliation(s)
- Simone A. De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Harley L. Worthy
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Christina Stracke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Nicholas J. Harmer
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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4
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McLaren M, Conners R, Isupov MN, Gil-Díez P, Gambelli L, Gold VAM, Walter A, Connell SR, Williams B, Daum B. CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state. Nat Microbiol 2023; 8:1834-1845. [PMID: 37709902 PMCID: PMC10522483 DOI: 10.1038/s41564-023-01469-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from the microsporidian parasite Spraguea lophii in situ by a combination of electron cryo-tomography and single-particle electron cryo-microscopy. We show that microsporidian spores contain hibernating ribosomes that are locked in a dimeric (100S) state, which is formed by a unique dimerization mechanism involving the beak region. The ribosomes within the dimer are fully assembled, suggesting that they are ready to be activated once the host cell is invaded. This study provides structural evidence for dimerization acting as a mechanism for ribosomal hibernation in microsporidia, and therefore demonstrates that eukaryotes utilize this mechanism in translational control.
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Affiliation(s)
- Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Michail N Isupov
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Patricia Gil-Díez
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Crop Science Centre, Cambridge University, Cambridge, UK
| | - Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Andreas Walter
- Center of Optical Technologies, Aalen University, Aalen, Germany
| | - Sean R Connell
- Structural Biology of Cellular Machines, IIS Biobizkaia, Barakaldo, Spain
| | - Bryony Williams
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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5
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Khazma T, Grossman A, Guez-Haddad J, Feng C, Dabas H, Sain R, Weitman M, Zalk R, Isupov MN, Hammarlund M, Hons M, Opatowsky Y. Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans. Cell Rep 2023; 42:113026. [PMID: 37635352 PMCID: PMC10675840 DOI: 10.1016/j.celrep.2023.113026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 06/05/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed in C. elegans (ceSARM/ceTIR-1). We hypothesized that differences in SARM between species might exist and account for the divergence in WD. We first show that expression of the human (h)SARM1, but not ceTIR-1, in C. elegans neurons is sufficient to confer axon degeneration after nerve injury. Next, we determined the cryoelectron microscopy structure of ceTIR-1 and found that, unlike hSARM1, which exists as an auto-inhibited ring octamer, ceTIR-1 forms a readily active 9-mer. Enzymatically, the NADase activity of ceTIR-1 is substantially weaker (10-fold higher Km) than that of hSARM1, and even when fully active, it falls short of consuming all cellular NAD+. Our experiments provide insight into the molecular mechanisms and evolution of SARM orthologs and WD across species.
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Affiliation(s)
- Tami Khazma
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Atira Grossman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Chengye Feng
- Departments of Neuroscience and Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hadas Dabas
- Departments of Neuroscience and Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Radhika Sain
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Weitman
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Ran Zalk
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Marc Hammarlund
- Departments of Neuroscience and Genetics, Yale School of Medicine, New Haven, CT, USA.
| | - Michael Hons
- European Molecular Biology Laboratory, Grenoble, France.
| | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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6
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Roy S, Vivoli Vega M, Ames JR, Britten N, Kent A, Evans K, Isupov MN, Harmer NJ. The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding. J Biol Chem 2023; 299:103033. [PMID: 36806680 PMCID: PMC10031466 DOI: 10.1016/j.jbc.2023.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.
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Affiliation(s)
| | | | | | | | - Amy Kent
- Living Systems Institute, Exeter, UK
| | - Kim Evans
- Living Systems Institute, Exeter, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Exeter, UK
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7
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Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG. CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:1079-1089. [PMID: 36048148 PMCID: PMC9435598 DOI: 10.1107/s2059798322007987] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.
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8
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Cross AR, Roy S, Vivoli Vega M, Rejzek M, Nepogodiev SA, Cliff M, Salmon D, Isupov MN, Field RA, Prior JL, Harmer NJ. Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. J Biol Chem 2022; 298:101903. [PMID: 35398092 PMCID: PMC9095892 DOI: 10.1016/j.jbc.2022.101903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii, respectively. Streptose forms the central moiety of the antibiotic streptomycin, while DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalyzed by the enzymes RmlA, RmlB, RmlC, and RmlD, but the exact mechanism is unclear. Streptose and DHHS biosynthesis unusually requires a ring contraction step that could be performed by orthologs of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii has identified StrM and CBU1838 proteins as RmlC orthologs in these respective species. Here, we demonstrate that both enzymes can perform the RmlC 3'',5'' double epimerization activity necessary to support TDP-rhamnose biosynthesis in vivo. This is consistent with the ring contraction step being performed on a double epimerized substrate. We further demonstrate that proton exchange is faster at the 3''-position than the 5''-position, in contrast to a previously studied ortholog. We additionally solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to those of the previously characterized enzymes RmlC, EvaD, and ChmJ. These results support the hypothesis that streptose and DHHS are biosynthesized using the TDP pathway and that an RmlD paralog most likely performs ring contraction following double epimerization. This work will support the elucidation of the full pathways for biosynthesis of these unique sugars.
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Affiliation(s)
- Alice R Cross
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mirella Vivoli Vega
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Matthew Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Debbie Salmon
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom; Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Joann L Prior
- Dstl, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom.
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9
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Gambelli L, Isupov MN, Conners R, McLaren M, Bellack A, Gold V, Rachel R, Daum B. An archaellum filament composed of two alternating subunits. Nat Commun 2022; 13:710. [PMID: 35132062 PMCID: PMC8821640 DOI: 10.1038/s41467-022-28337-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament’s flexibility. The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Vicki Gold
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK. .,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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10
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De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schönheit P, Littlechild JA. Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp. Front Bioeng Biotechnol 2021; 9:711487. [PMID: 34422783 PMCID: PMC8378251 DOI: 10.3389/fbioe.2021.711487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.
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Affiliation(s)
- Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andreas Reinhardt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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11
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Zhu C, Chen Y, Isupov MN, Littlechild JA, Sun L, Liu X, Wang Q, Gong H, Dong P, Zhang N, Wu Y. Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design. J Agric Food Chem 2021; 69:1079-1090. [PMID: 33445864 DOI: 10.1021/acs.jafc.0c06338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipolytic enzymes are essential biocatalysts in food processing as well as pharmaceutical and pesticide industries, catalyzing the cleavage of ester bonds in a variety of acyl chain substrates. Here, we report the crystal structure of an esterase from the deep-sea hydrothermal vent of the East Pacific Rise (EprEst). The X-ray structure of EprEst in complex with the ligand, acetate, has been determined at 2.03 Å resolution. The structure reveals a unique spatial arrangement and orientation of the helix cap domain and α/β hydrolase domain, which form a substrate pocket with preference for short-chain acyl groups. Molecular docking analysis further demonstrated that the active site pocket could accommodate p-nitrophenyl (pNP) carboxyl ligands of varying lengths (≤6 C atoms), with pNP-butyrate ester predicted to have the highest binding affinity. Additionally, the semirational design was conducted to improve the thermostability of EprEst by enzyme engineering based on the established structure and multiple sequence alignment. A mutation, K114P, introduced in the hinge region of the esterase, which displayed increased thermostability and enzyme activity. Collectively, the structural and functional data obtained herein could be used as basis for further protein engineering to ultimately expand the scope of industrial applications of marine-derived lipolytic enzymes.
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Affiliation(s)
- Chunhua Zhu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yayu Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Xiaodong Liu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Na Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
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12
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Yilmazer B, Isupov MN, De Rose SA, Bulut H, Benninghoff JC, Binay B, Littlechild JA. Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme. J Struct Biol 2020; 212:107657. [DOI: 10.1016/j.jsb.2020.107657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
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13
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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14
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Sporny M, Guez-Haddad J, Khazma T, Yaron A, Dessau M, Shkolnisky Y, Mim C, Isupov MN, Zalk R, Hons M, Opatowsky Y. Structural basis for SARM1 inhibition and activation under energetic stress. eLife 2020; 9:e62021. [PMID: 33185189 PMCID: PMC7688312 DOI: 10.7554/elife.62021] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/12/2020] [Indexed: 12/24/2022] Open
Abstract
SARM1, an executor of axonal degeneration, displays NADase activity that depletes the key cellular metabolite, NAD+, in response to nerve injury. The basis of SARM1 inhibition and its activation under stress conditions are still unknown. Here, we present cryo-EM maps of SARM1 at 2.9 and 2.7 Å resolutions. These indicate that SARM1 homo-octamer avoids premature activation by assuming a packed conformation, with ordered inner and peripheral rings, that prevents dimerization and activation of the catalytic domains. This inactive conformation is stabilized by binding of SARM1's own substrate NAD+ in an allosteric location, away from the catalytic sites. This model was validated by mutagenesis of the allosteric site, which led to constitutively active SARM1. We propose that the reduction of cellular NAD+ concentration contributes to the disassembly of SARM1's peripheral ring, which allows formation of active NADase domain dimers, thereby further depleting NAD+ to cause an energetic catastrophe and cell death.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Tami Khazma
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Avraham Yaron
- Department of Biomolecular Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Moshe Dessau
- Azrieli Faculty of Medicine, Bar Ilan UniversitySafedIsrael
| | - Yoel Shkolnisky
- Department of Applied Mathematics, School of Mathematical Sciences, Tel-Aviv UniversityTel-AvivIsrael
| | - Carsten Mim
- Royal Technical Institute (KTH), Dept. For Biomedical Engineering and Health SystemsStockholmSweden
| | | | - Ran Zalk
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the NegevBeer-ShevaIsrael
| | - Michael Hons
- European Molecular Biology LaboratoryGrenobleFrance
| | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
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15
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Wang Q, Jiang M, Isupov MN, Chen Y, Littlechild JA, Sun L, Wu X, Wang Q, Yang W, Chen L, Li Q, Wu Y. The crystal structure of Arabidopsis BON1 provides insights into the copine protein family. Plant J 2020; 103:1215-1232. [PMID: 32369638 DOI: 10.1111/tpj.14797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/17/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
The Arabidopsis thaliana BON1 gene product is a member of the evolutionary conserved eukaryotic calcium-dependent membrane-binding protein family. The copine protein is composed of two C2 domains (C2A and C2B) followed by a vWA domain. The BON1 protein is localized on the plasma membrane, and is known to suppress the expression of immune receptor genes and to positively regulate stomatal closure. The first structure of this protein family has been determined to 2.5-Å resolution and shows the structural features of the three conserved domains C2A, C2B and vWA. The structure reveals the third Ca2+ -binding region in C2A domain is longer than classical C2 domains and a novel Ca2+ binding site in the vWA domain. The structure of BON1 bound to Mn2+ is also presented. The binding of the C2 domains to phospholipid (PSF) has been modeled and provides an insight into the lipid-binding mechanism of the copine proteins. Furthermore, the selectivity of the separate C2A and C2B domains and intact BON1 to bind to different phospholipids has been investigated, and we demonstrated that BON1 could mediate aggregation of liposomes in response to Ca2+ . These studies have formed the basis of further investigations into the important role that the copine proteins play in vivo.
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Affiliation(s)
- Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Meiqin Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Michail N Isupov
- Henry Wellcome Center for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Yayu Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, P. R. China
| | - Jennifer A Littlechild
- Henry Wellcome Center for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, P. R. China
| | - Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qin Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, P. R. China
| | - Lifei Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, P. R. China
| | - Qi Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, P. R. China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, P. R. China
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16
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Sporny M, Guez-Haddad J, Lebendiker M, Ulisse V, Volf A, Mim C, Isupov MN, Opatowsky Y. Structural Evidence for an Octameric Ring Arrangement of SARM1. J Mol Biol 2019; 431:3591-3605. [PMID: 31278906 DOI: 10.1016/j.jmb.2019.06.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022]
Abstract
SARM1 induces axonal degeneration in response to various insults and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the integrity of the protein's SAM domains, as well as on the enzymatic conversion of NAD+ to ADPR (ADP Ribose) products by the SARM1's TIR domain. Therefore, inhibition of either SAM or TIR functions may constitute an effective therapeutic strategy. However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. In this study, we found that SARM1 assembles into an octameric ring. This arrangement was not described before in other SAM proteins, but is reminiscent of the apoptosome and inflammasome-well-known apoptotic ring-like oligomers. We show that both SARM1 and the isolated tandem SAM1-2 domains form octamers in solution, and electron microscopy analysis reveals an octameric ring of SARM1. We determined the crystal structure of SAM1-2 and found that it also forms a closed octameric ring in the crystal lattice. The SAM1-2 ring interactions are mediated by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between the neighboring protomers. We have mutated several interacting SAM1-2 interfaces and measured how these mutations affect SARM1 apoptotic activity in cultured cells, and in this way identified critical oligomerization sites that facilitate cell death. These results highlight the importance of oligomerization for SARM1 function and reveal critical epitopes for future targeted drug development.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Israel
| | - Valeria Ulisse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Allison Volf
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Carsten Mim
- Department of Biomedical Engineering and Health Solutions, Royal Technical Institute (KTH), Stockholm, Sweden; Department of Nutrition and Biosciences, Karolinska Institute, Huddinge, Sweden
| | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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17
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Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang Q, Wang Q, Yang W, Wu Y. Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1. FEBS J 2019; 286:2809-2821. [PMID: 30974511 DOI: 10.1111/febs.14846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/18/2019] [Accepted: 04/09/2019] [Indexed: 11/26/2022]
Abstract
The phosphate starvation response 1 (PHR1) protein has a central role in mediating the response to phosphate starvation in plants. PHR1 is composed of a number of domains including a MYB domain involved with DNA binding and a coiled-coil domain proposed to be involved with dimer formation. PHR1 binds to the promoter of phosphate starvation-induced genes to control the levels of phosphate required for nutrition. Previous studies have shown that both the MYB domain and the coiled-coil domain of PHR1 are required for binding the target DNA. Here, we describe the crystal structure of the PHR1 MYB domain and two structures of its complex with the PHR1-binding DNA sequence (P1BS). Structural and isothermal titration calorimetry has been carried out showing that the MYB domain of PHR1 alone is sufficient for target DNA recognition and binding. Two copies of the PHR1 MYB domain bind to the same major groove of the P1BS DNA with few direct interactions between the individual MYB domains. In addition, the PHR1 MYB-P1BS DNA complex structures reveal amino acid residues involved in DNA recognition and binding. Mutagenesis of these residues results in lost or impaired ability of PHR1 MYB to bind to its target DNA. The results presented reveal the structural basis for DNA recognition by the PHR1 MYB domain and demonstrate that two PHR1 MYB domains attach to their P1BS DNA targeting sequence. DATABASE: Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 6J4K (PHR1 MYB), 6J4R (PHR1 MYB-R-P1BS), 6J5B (MYB-CC-R2-P1BS).
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Affiliation(s)
- Meiqin Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK
| | | | - Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qin Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
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18
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Isupov MN, Boyko KM, Sutter JM, James P, Sayer C, Schmidt M, Schönheit P, Nikolaeva AY, Stekhanova TN, Mardanov AV, Ravin NV, Bezsudnova EY, Popov VO, Littlechild JA. Corrigendum: Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization. Front Bioeng Biotechnol 2019; 7:79. [PMID: 31058146 PMCID: PMC6477565 DOI: 10.3389/fbioe.2019.00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022] Open
Affiliation(s)
- Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konstantin M Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jan-Moritz Sutter
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marcel Schmidt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Alena Yu Nikolaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana N Stekhanova
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Vladimir O Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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19
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Barak R, Yom-Tov G, Guez-Haddad J, Gasri-Plotnitsky L, Maimon R, Cohen-Berkman M, McCarthy AA, Perlson E, Henis-Korenblit S, Isupov MN, Opatowsky Y. Structural Principles in Robo Activation and Auto-inhibition. Cell 2019; 177:272-285.e16. [PMID: 30853216 DOI: 10.1016/j.cell.2019.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/06/2018] [Accepted: 02/06/2019] [Indexed: 01/28/2023]
Abstract
Proper brain function requires high-precision neuronal expansion and wiring, processes controlled by the transmembrane Roundabout (Robo) receptor family and their Slit ligands. Despite their great importance, the molecular mechanism by which Robos' switch from "off" to "on" states remains unclear. Here, we report a 3.6 Å crystal structure of the intact human Robo2 ectodomain (domains D1-8). We demonstrate that Robo cis dimerization via D4 is conserved through hRobo1, 2, and 3 and the C. elegans homolog SAX-3 and is essential for SAX-3 function in vivo. The structure reveals two levels of auto-inhibition that prevent premature activation: (1) cis blocking of the D4 dimerization interface and (2) trans interactions between opposing Robo receptors that fasten the D4-blocked conformation. Complementary experiments in mouse primary neurons and C. elegans support the auto-inhibition model. These results suggest that Slit stimulation primarily drives the release of Robo auto-inhibition required for dimerization and activation.
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Affiliation(s)
- Reut Barak
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Galit Yom-Tov
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Roy Maimon
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Moran Cohen-Berkman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel.
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20
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Line K, Isupov MN, LaCourse EJ, Cutress DJ, Morphew RM, Brophy PM, Littlechild JA. X-ray structure of Fasciola hepatica Sigma class glutathione transferase 1 reveals a disulfide bond to support stability in gastro-intestinal environment. Sci Rep 2019; 9:902. [PMID: 30696975 PMCID: PMC6351632 DOI: 10.1038/s41598-018-37531-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/05/2018] [Indexed: 11/18/2022] Open
Abstract
Sigma class GST (Prostaglandin D synthase), FhGST-S1, is present in the excretory–secretory products (ES) of the liver fluke parasite Fasciola hepatica as cargo of extracellular vesicles (EVs) released by the parasite. FhGST-S1 has a well characterised role in the modulation of the immune response; a key fluke intercession that allows for establishment and development within their hosts. We have resolved the three-dimensional structure of FhGST-S1 in complex with its co-factor glutathione, in complex with a glutathione-cysteine adduct, and in a glutathione disulfide complex in order to initiate a research pipeline to mechanistically understand how FhGST-S1 functions within the host environment and to rationally design selective inhibitors. The overall fold of FhGST-S1 shows high structural similarity to other Sigma class GSTs. However, a unique interdomain disulfide bond was found in the FhGST-S1 which could stabilise the structure within the host gastro-intestinal environment. The position of the two domains of the protein with respect to each other is seen to be crucial in the formation of the active site cleft of the enzyme. The interdomain disulfide bond raises the possibility of oxidative regulation of the active site of this GST protein.
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Affiliation(s)
- Kirsty Line
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - E James LaCourse
- Liverpool School of Tropical Medicine, Liverpool, Pembroke Place, L3 5QA, UK
| | - David J Cutress
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Russell M Morphew
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Peter M Brophy
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DA, UK.
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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21
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Isupov MN, Boyko KM, Sutter JM, James P, Sayer C, Schmidt M, Schönheit P, Nikolaeva AY, Stekhanova TN, Mardanov AV, Ravin NV, Bezsudnova EY, Popov VO, Littlechild JA. Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization. Front Bioeng Biotechnol 2019; 7:7. [PMID: 30733943 PMCID: PMC6353796 DOI: 10.3389/fbioe.2019.00007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/08/2019] [Indexed: 11/25/2022] Open
Abstract
Two new thermophilic branched chain amino acid transaminases have been identified within the genomes of different hyper-thermophilic archaea, Geoglobus acetivorans, and Archaeoglobus fulgidus. These enzymes belong to the class IV of transaminases as defined by their structural fold. The enzymes have been cloned and over-expressed in Escherichia coli and the recombinant enzymes have been characterized both biochemically and structurally. Both enzymes showed high thermostability with optimal temperature for activity at 80 and 85°C, respectively. They retain good activity after exposure to 50% of the organic solvents, ethanol, methanol, DMSO and acetonitrile. The enzymes show a low activity to (R)-methylbenzylamine but no activity to (S)-methylbenzylamine. Both enzymes have been crystallized and their structures solved in the internal aldimine form, to 1.9 Å resolution for the Geoglobus enzyme and 2.0 Å for the Archaeoglobus enzyme. Also the Geoglobus enzyme structure has been determined in complex with the amino acceptor α-ketoglutarate and the Archaeoglobus enzyme in complex with the inhibitor gabaculine. These two complexes have helped to determine the conformation of the enzymes during enzymatic turnover and have increased understanding of their substrate specificity. A comparison has been made with another (R) selective class IV transaminase from the fungus Nectria haematococca which was previously studied in complex with gabaculine. The subtle structural differences between these enzymes has provided insight regarding their different substrate specificities.
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Affiliation(s)
- Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konstantin M. Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jan-Moritz Sutter
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marcel Schmidt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Alena Yu. Nikolaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey V. Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Vladimir O. Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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22
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Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP. The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA. J Biol Chem 2018; 293:19429-19440. [PMID: 30337369 DOI: 10.1074/jbc.ra118.005173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/16/2018] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of hicAB in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.
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Affiliation(s)
- Ashley J Winter
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Christopher Williams
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Michail N Isupov
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Hannah Crocker
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Mariya Gromova
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Philip Marsh
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Oliver J Wilkinson
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Mark S Dillingham
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Nicholas J Harmer
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Richard W Titball
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom,
| | - Matthew P Crump
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom,
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23
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Ferrandi EE, Sayer C, De Rose SA, Guazzelli E, Marchesi C, Saneei V, Isupov MN, Littlechild JA, Monti D. New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments. Front Bioeng Biotechnol 2018; 6:144. [PMID: 30386778 PMCID: PMC6198070 DOI: 10.3389/fbioe.2018.00144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli, purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis-2,3-epoxybutane producing the (2R,3R)-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4R)-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.
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Affiliation(s)
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Elisa Guazzelli
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Carlotta Marchesi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Vahid Saneei
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
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24
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Knight AR, Taylor EL, Lukaszewski R, Jensen KT, Jones HE, Carré JE, Isupov MN, Littlechild JA, Bailey SJ, Brewer E, McDonald TJ, Pitt AR, Spickett CM, Winyard PG. A high-sensitivity electrochemiluminescence-based ELISA for the measurement of the oxidative stress biomarker, 3-nitrotyrosine, in human blood serum and cells. Free Radic Biol Med 2018; 120:246-254. [PMID: 29555590 DOI: 10.1016/j.freeradbiomed.2018.03.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 02/02/2023]
Abstract
The generation of 3-nitrotyrosine, within proteins, is a post-translational modification resulting from oxidative or nitrative stress. It has been suggested that this modification could be used as a biomarker for inflammatory diseases. Despite the superiority of mass spectrometry-based determinations of nitrotyrosine, in a high-throughput clinical setting the measurement of nitrotyrosine by an enzyme-linked immunosorbent assay (ELISA) is likely to be more cost-effective. ELISAs offer an alternative means to detect nitrotyrosine, but many commercially available ELISAs are insufficiently sensitive to detect nitrotyrosine in healthy human serum. Here, we report the development, validation and clinical application of a novel electrochemiluminescence-based ELISA for nitrotyrosine which provides superior sensitivity (e.g. a 50-fold increase in sensitivity compared with one of the tested commercial colorimetric ELISAs). This nitrotyrosine ELISA has the following characteristics: a lower limit of quantitation of 0.04 nM nitrated albumin equivalents; intra- and inter-assay coefficients of variation of 6.5% and 11.3%, respectively; a mean recovery of 106 ± 3% and a mean linearity of 0.998 ± 0.001. Far higher nitration levels were measured in normal human blood cell populations when compared to plasma. Mass spectrometry was used to validate the new ELISA method. The analysis of the same set of chemically modified albumin samples using the ELISA method and mass spectrometry showed good agreement for the relative levels of nitration present in each sample. The assay was applied to serum samples from patients undergoing elective surgery which induces the human inflammatory response. Matched samples were collected before and one day after surgery. An increase in nitration was detected following surgery (median (IQR): 0.59 (0.00-1.34) and 0.97 (0.00-1.70) nitrotyrosine (fmol of nitrated albumin equivalents/mg protein) for pre- and post-surgery respectively. The reported assay is suitable for nitrotyrosine determination in patient serum samples, and may also be applicable as a means to determine oxidative stress in primary and cultured cell populations.
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Affiliation(s)
- Annie R Knight
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Emma L Taylor
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | | | - Karina Tveen Jensen
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Helen E Jones
- CBR Division, Dstl, Porton Down, Salisbury SP4 0JQ, UK
| | - Jane E Carré
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Stephen J Bailey
- Sport and Health Sciences, Richards Building, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Emily Brewer
- Clinical Chemistry, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy J McDonald
- Clinical Chemistry, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Paul G Winyard
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK.
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25
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Isupov MN, Schröder E, Gibson RP, Beecher J, Donadio G, Saneei V, Dcunha SA, McGhie EJ, Sayer C, Davenport CF, Lau PCK, Hasegawa Y, Iwaki H, Kadow M, Balke K, Bornscheuer UT, Bourenkov G, Littlechild JA. The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase. Corrigendum. Acta Crystallogr D Struct Biol 2018; 74:379. [PMID: 29652264 DOI: 10.1107/s205979831800150x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A statement is amended in the article by Isupov et al. [(2015). Acta Cryst. D71, 2344-2353].
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Affiliation(s)
- Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Ewald Schröder
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Robert P Gibson
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Jean Beecher
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Giuliana Donadio
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Vahid Saneei
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Stephlina A Dcunha
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Emma J McGhie
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Colin F Davenport
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Peter C K Lau
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
| | - Yoshie Hasegawa
- Department of Biotechnology, Faculty of Engineering, Kansai University, Japan
| | - Hiroaki Iwaki
- Department of Biotechnology, Faculty of Engineering, Kansai University, Japan
| | - Maria Kadow
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Kathleen Balke
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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26
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Sporny M, Guez-Haddad J, Kreusch A, Shakartzi S, Neznansky A, Cross A, Isupov MN, Qualmann B, Kessels MM, Opatowsky Y. Structural History of Human SRGAP2 Proteins. Mol Biol Evol 2017; 34:1463-1478. [PMID: 28333212 PMCID: PMC5435084 DOI: 10.1093/molbev/msx094] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In the development of the human brain, human-specific genes are considered to play key roles, conferring its unique advantages and vulnerabilities. At the time of Homo lineage divergence from Australopithecus, SRGAP2C gradually emerged through a process of serial duplications and mutagenesis from ancestral SRGAP2A (3.4–2.4 Ma). Remarkably, ectopic expression of SRGAP2C endows cultured mouse brain cells, with human-like characteristics, specifically, increased dendritic spine length and density. To understand the molecular mechanisms underlying this change in neuronal morphology, we determined the structure of SRGAP2A and studied the interplay between SRGAP2A and SRGAP2C. We found that: 1) SRGAP2A homo-dimerizes through a large interface that includes an F-BAR domain, a newly identified F-BAR extension (Fx), and RhoGAP-SH3 domains. 2) SRGAP2A has an unusual inverse geometry, enabling associations with lamellipodia and dendritic spine heads in vivo, and scaffolding of membrane protrusions in cell culture. 3) As a result of the initial partial duplication event (∼3.4 Ma), SRGAP2C carries a defective Fx-domain that severely compromises its solubility and membrane-scaffolding ability. Consistently, SRGAP2A:SRAGP2C hetero-dimers form, but are insoluble, inhibiting SRGAP2A activity. 4) Inactivation of SRGAP2A is sensitive to the level of hetero-dimerization with SRGAP2C. 5) The primal form of SRGAP2C (P-SRGAP2C, existing between ∼3.4 and 2.4 Ma) is less effective in hetero-dimerizing with SRGAP2A than the modern SRGAP2C, which carries several substitutions (from ∼2.4 Ma). Thus, the genetic mutagenesis phase contributed to modulation of SRGAP2A’s inhibition of neuronal expansion, by introducing and improving the formation of inactive SRGAP2A:SRGAP2C hetero-dimers, indicating a stepwise involvement of SRGAP2C in human evolutionary history.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Annett Kreusch
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Sivan Shakartzi
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avi Neznansky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Alice Cross
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Britta Qualmann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Michael M Kessels
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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27
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Zhang J, Fan F, Zhao Y, Sun L, Liu Y, Keegan RM, Isupov MN, Wu Y. Crystal structure of the type IV secretion system component CagX from Helicobacter pylori. Acta Crystallogr F Struct Biol Commun 2017; 73:167-173. [PMID: 28291753 PMCID: PMC5349311 DOI: 10.1107/s2053230x17001376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/26/2017] [Indexed: 12/28/2022]
Abstract
The structure of the C-terminal domain of CagX is presented and structural comparisons with TraO, its homologue from another bacterial T4S system, reveal distinct and conserved features. Helicobacter pylori, a Gram-negative bacterial pathogen prevalent in the human population, is the causative agent of severe gastric diseases. An H. pylori type IV secretion (T4S) system encoded by the cytotoxin-associated gene pathogenicity island (cagPAI) is responsible for communication with host cells. As a component of the cagPAI T4S system core complex, CagX plays an important role in virulence-protein translocation into the host cells. In this work, the crystal structure of the C-terminal domain of CagX (CagXct), which is a homologue of the VirB9 protein from the VirB/D4 T4S system, is presented. CagXct is only the second three-dimensional structure to be elucidated of a VirB9-like protein. Another homologue, TraO, which is encoded on the Escherichia coli conjugative plasmid pKM101, shares only 19% sequence identity with CagXct; however, there is a remarkable similarity in tertiary structure between these two β-sandwich protein domains. Most of the residues that are conserved between CagXct and TraO are located within the protein core and appear to be responsible for the preservation of this domain fold. The studies presented here will contribute to our understanding of different bacterial T4S systems.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002, People's Republic of China
| | - Fei Fan
- Fujian Health College, Fuzhou 350101, People's Republic of China
| | - Yanhe Zhao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002, People's Republic of China
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002, People's Republic of China
| | - Yadan Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002, People's Republic of China
| | - Ronan M Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, England
| | - Yunkun Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002, People's Republic of China
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Sporny M, Guez-Haddad J, Waterman DG, Isupov MN, Opatowsky Y. Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain. Acta Crystallogr D Struct Biol 2016; 72:1241-1253. [PMID: 27917825 DOI: 10.1107/s2059798316016697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
SRGAP2 (Slit-Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein. Diffraction data were collected from two significantly non-isomorphous crystals in the same monoclinic C2 space group. A correct molecular-replacment solution was obtained by applying a molecular symmetry-constrained systematic search approach that took advantage of the conserved biological symmetry of the F-BAR domains. It is shown that similar approaches can solve other F-BAR structures that were previously determined by experimental phasing. Diffraction data were reprocessed with a high-resolution cutoff of 2.2 Å, chosen using less strict statistical criteria. This has improved the outcome of multi-crystal averaging and other density-modification procedures.
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Affiliation(s)
- Michael Sporny
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Julia Guez-Haddad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | | | | | - Yarden Opatowsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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Vivoli M, Isupov MN, Nicholas R, Hill A, Scott AE, Kosma P, Prior JL, Harmer NJ. Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery. ACTA ACUST UNITED AC 2016; 22:1622-32. [PMID: 26687481 PMCID: PMC4691232 DOI: 10.1016/j.chembiol.2015.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/20/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Gram-negative bacteria utilize heptoses as part of their repertoire of extracellular polysaccharide virulence determinants. Disruption of heptose biosynthesis offers an attractive target for novel antimicrobials. A critical step in the synthesis of heptoses is their 1-O phosphorylation, mediated by kinases such as HldE or WcbL. Here, we present the structure of WcbL from Burkholderia pseudomallei. We report that WcbL operates through a sequential ordered Bi-Bi mechanism, loading the heptose first and then ATP. We show that dimeric WcbL binds ATP anti-cooperatively in the absence of heptose, and cooperatively in its presence. Modeling of WcbL suggests that heptose binding causes an elegant switch in the hydrogen-bonding network, facilitating the binding of a second ATP molecule. Finally, we screened a library of drug-like fragments, identifying hits that potently inhibit WcbL. Our results provide a novel mechanism for control of substrate binding and emphasize WcbL as an attractive anti-microbial target for Gram-negative bacteria.
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Affiliation(s)
- Mirella Vivoli
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca Nicholas
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Hill
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew E Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Paul Kosma
- University of Natural Resources and Life Sciences-Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Joann L Prior
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK.
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Zarafeta D, Kissas D, Sayer C, Gudbergsdottir SR, Ladoukakis E, Isupov MN, Chatziioannou A, Peng X, Littlechild JA, Skretas G, Kolisis FN. Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate. PLoS One 2016; 11:e0146454. [PMID: 26741138 PMCID: PMC4704807 DOI: 10.1371/journal.pone.0146454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitrios Kissas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Sayer C, Szabo Z, Isupov MN, Ingham C, Littlechild JA. The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. Front Microbiol 2015; 6:1294. [PMID: 26635762 PMCID: PMC4655241 DOI: 10.3389/fmicb.2015.01294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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Isupov MN, Schröder E, Gibson RP, Beecher J, Donadio G, Saneei V, Dcunha SA, McGhie EJ, Sayer C, Davenport CF, Lau PC, Hasegawa Y, Iwaki H, Kadow M, Balke K, Bornscheuer UT, Bourenkov G, Littlechild JA. The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase. ACTA ACUST UNITED AC 2015; 71:2344-53. [PMID: 26527149 PMCID: PMC4631483 DOI: 10.1107/s1399004715017939] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022]
Abstract
The first crystal structure of a type II Baeyer–Villiger monooxygenase reveals a different ring orientation of its FMN cofactor compared with other related bacterial luciferase-family enzymes. The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer–Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.
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Affiliation(s)
- Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Ewald Schröder
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Robert P Gibson
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Jean Beecher
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Giuliana Donadio
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Vahid Saneei
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Stephlina A Dcunha
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Emma J McGhie
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Colin F Davenport
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Peter C Lau
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
| | - Yoshie Hasegawa
- Department of Biotechnology, Faculty of Engineering, Kansai University, Japan
| | - Hiroaki Iwaki
- Department of Biotechnology, Faculty of Engineering, Kansai University, Japan
| | - Maria Kadow
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Kathleen Balke
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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33
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Sayer C, Isupov MN, Bonch-Osmolovskaya E, Littlechild JA. Structural studies of a thermophilic esterase from a new Planctomycetes species, Thermogutta terrifontis. FEBS J 2015; 282:2846-57. [PMID: 26011036 DOI: 10.1111/febs.13326] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/08/2015] [Accepted: 05/19/2015] [Indexed: 11/28/2022]
Abstract
Thermogutta terrifontis esterase (TtEst), a carboxyl esterase identified in the novel thermophilic bacterium T. terrifontis from the phylum Planctomycetes, has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity towards small p-nitrophenyl (pNP) carboxylic esters, with optimal activity for pNP-propionate. The enzyme retained 95% activity after incubation for 1 h at 80 °C. The crystal structures of the native TtEst and its complexes with the substrate analogue D-malate and the product acetate have been determined to high resolution. The bound ligands have allowed the identification of the carboxyl and alcohol binding pockets in the enzyme active site. Comparison of TtEst with structurally related enzymes provides insight into how differences in their catalytic activity can be rationalized based upon the properties of the amino acid residues in their active site pockets. The mutant enzymes L37A and L251A have been constructed to extend the substrate range of TtEst towards the larger butyrate and valerate pNP-esters. These mutant enzymes have also shown a significant increase in activity towards acetate and propionate pNP esters. A crystal structure of the L37A mutant was determined with the butyrate product bound in the carboxyl pocket of the active site. The mutant structure shows an expansion of the pocket that binds the substrate carboxyl group, which is consistent with the observed increase in activity towards pNP-butyrate.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
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34
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Ferrandi EE, Sayer C, Isupov MN, Annovazzi C, Marchesi C, Iacobone G, Peng X, Bonch-Osmolovskaya E, Wohlgemuth R, Littlechild JA, Monti D. Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. FEBS J 2015; 282:2879-94. [PMID: 26032250 DOI: 10.1111/febs.13328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 11/28/2022]
Abstract
The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specificity and stereoselectivity of these new LEH enzymes, which has been supported by mutagenesis studies.
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Affiliation(s)
- Erica Elisa Ferrandi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy.,University of Copenhagen, Denmark
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Celeste Annovazzi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Carlotta Marchesi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Gianluca Iacobone
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Xu Peng
- University of Copenhagen, Denmark
| | | | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
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35
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James P, Isupov MN, Sayer C, Saneei V, Berg S, Lioliou M, Kotlar HK, Littlechild JA. The structure of a tetrameric α-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides that contribute to its thermostability. ACTA ACUST UNITED AC 2014; 70:2607-18. [PMID: 25286845 DOI: 10.1107/s1399004714016526] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/16/2014] [Indexed: 11/10/2022]
Abstract
Carbonic anhydrase enzymes catalyse the reversible hydration of carbon dioxide to bicarbonate. A thermophilic Thermovibrio ammonificans α-carbonic anhydrase (TaCA) has been expressed in Escherichia coli and structurally and biochemically characterized. The crystal structure of TaCA has been determined in its native form and in two complexes with bound inhibitors. The tetrameric enzyme is stabilized by a unique core in the centre of the molecule formed by two intersubunit disulfides and a single lysine residue from each monomer that is involved in intersubunit ionic interactions. The structure of this core protects the intersubunit disulfides from reduction, whereas the conserved intrasubunit disulfides are not formed in the reducing environment of the E. coli host cytosol. When oxidized to mimic the environment of the periplasmic space, TaCA has increased thermostability, retaining 90% activity after incubation at 70°C for 1 h, making it a good candidate for industrial carbon-dioxide capture. The reduction of all TaCA cysteines resulted in dissociation of the tetrameric molecule into monomers with lower activity and reduced thermostability. Unlike other characterized α-carbonic anhydrases, TaCA does not display esterase activity towards p-nitrophenyl acetate, which appears to result from the increased rigidity of its protein scaffold.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Vahid Saneei
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Svein Berg
- Statoil Research Centre, Statoil, Arkitekt Ebbells veg 10, Rotvoll, 7005 Trondheim, Norway
| | - Maria Lioliou
- Statoil Research Centre, Statoil, Arkitekt Ebbells veg 10, Rotvoll, 7005 Trondheim, Norway
| | - Hans Kristian Kotlar
- Statoil Research Centre, Statoil, Arkitekt Ebbells veg 10, Rotvoll, 7005 Trondheim, Norway
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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Lebedev AA, Isupov MN. Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda. ACTA ACUST UNITED AC 2014; 70:2430-43. [PMID: 25195756 DOI: 10.1107/s1399004714014795] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/23/2014] [Indexed: 11/10/2022]
Abstract
The presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the R(free) ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics.
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Affiliation(s)
- Andrey A Lebedev
- CCP4, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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Sayer C, Martinez-Torres RJ, Richter N, Isupov MN, Hailes HC, Littlechild JA, Ward JM. The substrate specificity, enantioselectivity and structure of the (R)-selective amine : pyruvate transaminase from Nectria haematococca. FEBS J 2014; 281:2240-53. [PMID: 24618038 PMCID: PMC4255305 DOI: 10.1111/febs.12778] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/30/2022]
Abstract
During the last decade the use of transaminases for the production of pharmaceutical and fine chemical intermediates has attracted a great deal of attention. Transaminases are versatile biocatalysts for the efficient production of amine intermediates and many have (S)-enantiospecificity. Transaminases with (R)-specificity are needed to expand the applications of these enzymes in biocatalysis. In this work we have identified a fungal putative (R)-specific transaminase from the Eurotiomycetes Nectria haematococca, cloned a synthetic version of this gene, demonstrated (R)-selective deamination of several substrates including (R)-α-methylbenzylamine, as well as production of (R)-amines, and determined its crystal structure. The crystal structures of the holoenzyme and the complex with an inhibitor gabaculine offer the first detailed insight into the structural basis for substrate specificity and enantioselectivity of the industrially important class of (R)-selective amine : pyruvate transaminases.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, College of Life and Environmental Sciences, University of Exeter, EX4 4QD, UK
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Novak HR, Sayer C, Isupov MN, Gotz D, Spragg AM, Littlechild JA. Biochemical and structural characterisation of a haloalkane dehalogenase from a marineRhodobacteraceae. FEBS Lett 2014; 588:1616-22. [DOI: 10.1016/j.febslet.2014.02.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
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Vivoli M, Ayres E, Beaumont E, Isupov MN, Harmer NJ. Structural insights into WcbI, a novel polysaccharide-biosynthesis enzyme. IUCrJ 2014; 1:28-38. [PMID: 25075317 PMCID: PMC4104973 DOI: 10.1107/s205225251302695x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/30/2013] [Indexed: 06/03/2023]
Abstract
Capsular polysaccharides (CPSs) are protective structures on the surfaces of many Gram-negative bacteria. The principal CPS of the human pathogen and Tier 1 select agent Burkholderia pseudomallei consists of a linear repeat of --3)--2-O-acetyl-6-deoxy-β-d-manno-heptopyranose-(1-. This CPS is critical to the virulence of this emerging pathogen and represents a key target for the development of novel therapeutics. wcbI is one of several genes in the CPS biosynthetic cluster whose deletion leads to significant attenuation of the pathogen; unlike most others, it has no homologues of known function and no detectable sequence similarity to any protein with an extant structure. Here, the crystal structure of WcbI bound to its proposed product, coenzyme A, is reported at 1.38 Å resolution, solved using the halide-soak method with multiple anomalous dispersion. This structure reveals that WcbI incorporates a previously described 100-amino-acid subdomain into a novel, principally helical fold (310 amino acids). This fold adopts a cradle-like structure, with a deep binding pocket for CoA in the loop-rich cradle. Structural analysis and biophysical assays suggest that WcbI functions as an acetyltransferase enzyme, whilst biochemical tests suggest that another functional module might be required to assist its activity in forming the mature B. pseudomallei capsule.
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Affiliation(s)
- Mirella Vivoli
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England
| | - Emily Ayres
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England
| | - Edward Beaumont
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England
| | - Michail N. Isupov
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England
| | - Nicholas J. Harmer
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England
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Sayer C, Isupov MN, Westlake A, Littlechild JA. Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. Acta Crystallogr D Biol Crystallogr 2013; 69:564-76. [PMID: 23519665 PMCID: PMC3606037 DOI: 10.1107/s0907444912051670] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022]
Abstract
The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Aaron Westlake
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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Novak HR, Sayer C, Isupov MN, Paszkiewicz K, Gotz D, Spragg AM, Littlechild JA. Marine Rhodobacteraceae L-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water. FEBS J 2013; 280:1664-80. [PMID: 23384397 DOI: 10.1111/febs.12177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/25/2013] [Accepted: 02/01/2013] [Indexed: 11/30/2022]
Abstract
The putative L-haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown to be an L-haloacid dehalogenase with highest activity towards brominated substrates with short carbon chains (≤ C3). The optimal temperature for enzyme activity was 55 °C, and the Vmax and Km were 1.75 μm·min(-1) ·mg(-1) of protein and 6.72 mm, respectively, when using monobromoacetic acid as a substrate. DehRhb showed moderate thermal stability, with a melting temperature of 67 °C. The enzyme demonstrated high tolerance to solvents, as shown by thermal shift experiments and solvent incubation assays. The DehRhb protein was crystallized and structures of the native, reaction intermediate and substrate-bound forms were determined. The active site of DehRhb had significant differences from previously studied L-haloacid dehalogenases. The asparagine and arginine residues shown to be essential for catalytic activity in other L-haloacid dehalogenases are not present in DehRhb. The histidine residue which replaces the asparagine residue in DehRhb was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine. The His/Glu dyad is positioned for deprotonation of the catalytic water which attacks the ester bond in the reaction intermediate. The catalytic water in DehRhb is shifted by ~ 1.5 Å from its position in other L-haloacid dehalogenases. A similar His/Glu or Asp dyad is known to activate the catalytic water in haloalkane dehalogenases. The DehRhb enzyme represents a novel member within the L-haloacid dehalogenase family and it has potential to be used as a commercial biocatalyst.
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Affiliation(s)
- Halina R Novak
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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Lebedev AA, Young P, Isupov MN, Moroz OV, Vagin AA, Murshudov GN. JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr D Biol Crystallogr 2012; 68:431-40. [PMID: 22505263 PMCID: PMC3322602 DOI: 10.1107/s090744491200251x] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/19/2012] [Indexed: 12/30/2022]
Abstract
Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user's additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user's library and generate new monomer entries is described, as well as new entries for links and associated modifications.
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Affiliation(s)
- Andrey A Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, England.
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Urusova DV, Isupov MN, Antonyuk S, Kachalova GS, Obmolova G, Vagin AA, Lebedev AA, Burenkov GP, Dauter Z, Bartunik HD, Lamzin VS, Melik-Adamyan WR, Mueller TD, Schnackerz KD. Crystal structure of D-serine dehydratase from Escherichia coli. Biochim Biophys Acta 2011; 1824:422-32. [PMID: 22197591 DOI: 10.1016/j.bbapap.2011.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 10/26/2011] [Accepted: 10/31/2011] [Indexed: 10/14/2022]
Abstract
D-Serine dehydratase from Escherichia coli is a member of the β-family (fold-type II) of the pyridoxal 5'-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydratase has been solved to 1.97Å-resolution for an orthorhombic data set by molecular replacement. In addition, the structure was refined in a monoclinic data set to 1.55Å resolution. The structure of DSD reveals a larger pyridoxal 5'-phosphate-binding domain and a smaller domain. The active site of DSD is very similar to those of the other members of the β-family. Lys118 forms the Schiff base to PLP, the cofactor phosphate group is liganded to a tetraglycine cluster Gly279-Gly283, and the 3-hydroxyl group of PLP is liganded to Asn170 and N1 to Thr424, respectively. In the closed conformation the movement of the small domain blocks the entrance to active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD suggests that the hydroxyl group of D-serine is coordinated to the carboxyl group of Asp238. The carboxyl oxygen of D-serine is coordinated to the hydroxyl group of Ser167 and the amide group of Leu171 (O1), whereas the O2 of the carboxyl group of D-serine is hydrogen-bonded to the hydroxyl group of Ser167 and the amide group of Thr168. A catalytic mechanism very similar to that proposed for L-serine dehydratase is discussed.
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Affiliation(s)
- Darya V Urusova
- The Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
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Shevtsov MB, Chen Y, Isupov MN, Leech A, Gollnick P, Antson AA. Bacillus licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers. J Struct Biol 2010; 170:127-33. [PMID: 20138150 PMCID: PMC2896485 DOI: 10.1016/j.jsb.2010.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/21/2010] [Accepted: 01/23/2010] [Indexed: 01/07/2023]
Abstract
Anti-TRAP (AT) protein regulates expression of tryptophan biosynthetic genes by binding to the trp RNA-binding attenuation protein (TRAP) and preventing its interaction with RNA. Bacillus subtilis AT forms trimers that can either interact with TRAP or can further assemble into dodecameric particles. To determine which oligomeric forms are preserved in AT proteins of other Bacilli we studied Bacillus licheniformis AT which shares 66% sequence identity with the B. subtilis protein. We show that in solution B. licheniformis AT forms stable trimers. In crystals, depending on pH, such trimers assemble into two different types of dodecameric particles, both having 23 point group symmetry. The dodecamer formed at pH 6.0 has the same conformation as previously observed for B. subtilis AT. This dodecamer contains a large internal chamber with the volume of approximately 700 A(3), which is lined by the side chains of twelve valine residues. The presence of the hydrophobic chamber hints at the possibility that the dodecamer formation could be induced by binding of a ligand. Interestingly, in the dodecamer formed at pH 8.0 all trimers are turned inside out relatively to the form observed at pH 6.0.
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Affiliation(s)
- Mikhail B. Shevtsov
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO1 5YW, UK
| | - Yanling Chen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Michail N. Isupov
- School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Leech
- Department of Biology, University of York, Heslington, York YO1 5DD, UK
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO1 5YW, UK,Corresponding author. Fax: +44 1904 328266.
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Ng CL, Waterman DG, Koonin EV, Walters AD, Chong JPJ, Isupov MN, Lebedev AA, Bunka DHJ, Stockley PG, Ortiz-Lombardía M, Antson AA. Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein. BMC Struct Biol 2009; 9:32. [PMID: 19454024 PMCID: PMC2695463 DOI: 10.1186/1472-6807-9-32] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 05/19/2009] [Indexed: 01/06/2023]
Abstract
Background Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown. Results We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner. Conclusion It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function.
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Affiliation(s)
- C Leong Ng
- York Structural Biology Laboratory, Chemistry Department, University of York, York, YO10 5YW, UK.
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Rye CA, Isupov MN, Lebedev AA, Littlechild JA. Biochemical and structural studies of a L-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii. Extremophiles 2008; 13:179-90. [PMID: 19039518 DOI: 10.1007/s00792-008-0208-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 10/29/2008] [Indexed: 11/26/2022]
Abstract
Haloacid dehalogenases have potential applications in the pharmaceutical and fine chemical industry as well as in the remediation of contaminated land. The L: -2-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned and over-expressed in Escherichia coli and successfully purified to homogeneity. Here we report the structure of the recombinant dehalogenase solved by molecular replacement in two different crystal forms. The enzyme is a homodimer with each monomer being composed of a core-domain of a beta-sheet bundle surrounded by alpha-helices and an alpha-helical sub-domain. This fold is similar to previously solved mesophilic L: -haloacid dehalogenase structures. The monoclinic crystal form contains a putative inhibitor L: -lactate in the active site. The enzyme displays haloacid dehalogenase activity towards carboxylic acids with the halide attached at the C2 position with the highest activity towards chloropropionic acid. The enzyme is thermostable with maximum activity at 60 degrees C and a half-life of over 1 h at 70 degrees C. The enzyme is relatively stable to solvents with 25% activity lost when incubated for 1 h in 20% v/v DMSO.
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Affiliation(s)
- Carrie A Rye
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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47
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Isupov MN, Lebedev AA. NCS-constrained exhaustive search using oligomeric models. Acta Crystallogr D Biol Crystallogr 2007; 64:90-8. [PMID: 18094472 PMCID: PMC2394828 DOI: 10.1107/s0907444907053802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 10/29/2007] [Indexed: 11/10/2022]
Abstract
The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.
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Affiliation(s)
- Michail N Isupov
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England.
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Sanders CM, Kovalevskiy OV, Sizov D, Lebedev AA, Isupov MN, Antson AA. Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors. Nucleic Acids Res 2007; 35:6451-7. [PMID: 17881379 PMCID: PMC2095799 DOI: 10.1093/nar/gkm705] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.
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Affiliation(s)
- Cyril M. Sanders
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Oleg V. Kovalevskiy
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Dmytro Sizov
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Andrey A. Lebedev
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Michail N. Isupov
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Alfred A. Antson
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- *To whom correspondence should be addressed. +44 1904328255+44 1904328266
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Rye CA, Isupov MN, Lebedev AA, Littlechild JA. An order–disorder twin crystal ofL-2-haloacid dehalogenase fromSulfolobus tokodaii. Acta Crystallogr D Biol Crystallogr 2007; 63:926-30. [PMID: 17642519 DOI: 10.1107/s0907444907026315] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 05/29/2007] [Indexed: 11/10/2022]
Abstract
The L-2-haloacid dehalogenase enzymes catalyse the hydrolytic cleavage of a halogen from the C2 position of short-chain haloacids. The recombinant dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned, overexpressed and purified to homogeneity. The 24 kDa enzyme was crystallized using the microbatch method in the monoclinic space group C2, with unit-cell parameters a = 127.6, b = 58.1, c = 51.2 A, beta = 97.2 degrees . Data were collected to 1.9 A resolution using synchrotron radiation and the structure was solved by molecular replacement. Analysis of the data and the preliminary refined model showed that the crystal was an order-disorder twin by reticular merohedry with a twin index of 10. It was possible to de-twin the experimental data utilizing the symmetry of the molecular layers from which the crystal is built.
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Affiliation(s)
- Carrie A Rye
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, England
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50
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Sayer C, Isupov MN, Littlechild JA. Crystallization and preliminary X-ray diffraction analysis of omega-amino acid:pyruvate transaminase from Chromobacterium violaceum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:117-9. [PMID: 17277454 PMCID: PMC2330129 DOI: 10.1107/s1744309107000863] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 01/08/2007] [Indexed: 05/13/2023]
Abstract
The enzyme omega-transaminase catalyses the conversion of chiral omega-amines to ketones. The recombinant enzyme from Chromobacterium violaceum has been purified to homogeneity. The enzyme was crystallized from PEG 4000 using the microbatch method. Data were collected to 1.7 A resolution from a crystal belonging to the triclinic space group P1, with unit-cell parameters a = 58.9, b = 61.9, c = 63.9 A, alpha = 71.9, beta = 87.0, gamma = 74.6 degrees . Data were also collected to 1.95 A from a second triclinic crystal form. The structure has been solved using the molecular-replacement method.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Exeter EX4 4QD, England
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Exeter EX4 4QD, England
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Exeter EX4 4QD, England
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