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Cowton VM, Owsianka AM, Fadda V, Ortega-Prieto AM, Cole SJ, Potter JA, Skelton JK, Jeffrey N, Di Lorenzo C, Dorner M, Taylor GL, Patel AH. Development of a structural epitope mimic: an idiotypic approach to HCV vaccine design. NPJ Vaccines 2021; 6:7. [PMID: 33420102 PMCID: PMC7794244 DOI: 10.1038/s41541-020-00269-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/01/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
HCV vaccine development is stymied by the high genetic diversity of the virus and the variability of the envelope glycoproteins. One strategy to overcome this is to identify conserved, functionally important regions—such as the epitopes of broadly neutralizing antibodies (bNAbs)—and use these as a basis for structure-based vaccine design. Here, we report an anti-idiotype approach that has generated an antibody that mimics a highly conserved neutralizing epitope on HCV E2. Crucially, a mutagenesis screen was used to identify the antibody, designated B2.1 A, whose binding characteristics to the bNAb AP33 closely resemble those of the original antigen. Protein crystallography confirmed that B2.1 A is a structural mimic of the AP33 epitope. When used as an immunogen B2.1 A induced antibodies that recognized the same epitope and E2 residues as AP33 and most importantly protected against HCV challenge in a mouse model.
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Affiliation(s)
- Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Ania M Owsianka
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Valeria Fadda
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | | | - Sarah J Cole
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Jane A Potter
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | - Jessica K Skelton
- Section of Virology, Department of Medicine, Imperial College London, London, UK
| | - Nathan Jeffrey
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Caterina Di Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Marcus Dorner
- Section of Virology, Department of Medicine, Imperial College London, London, UK
| | - Garry L Taylor
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK.
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Zaitsev V, Johnsen U, Reher M, Ortjohann M, Taylor GL, Danson MJ, Schönheit P, Crennell SJ. Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate. Biochemistry 2018; 57:3797-3806. [PMID: 29812914 DOI: 10.1021/acs.biochem.8b00535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 Å and that of KDG-aldolase from P. torridus at 2.50 Å resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage.
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Affiliation(s)
- Viatcheslav Zaitsev
- Biomolecular Sciences , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie , Christian-Albrechts-Universität , D-24118 Kiel , Germany
| | - Matthias Reher
- Institut für Allgemeine Mikrobiologie , Christian-Albrechts-Universität , D-24118 Kiel , Germany
| | - Marius Ortjohann
- Institut für Allgemeine Mikrobiologie , Christian-Albrechts-Universität , D-24118 Kiel , Germany
| | - Garry L Taylor
- Biomolecular Sciences , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| | - Michael J Danson
- Department of Biology & Biochemistry , University of Bath , Bath BA2 7AY , U.K
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie , Christian-Albrechts-Universität , D-24118 Kiel , Germany
| | - Susan J Crennell
- Department of Biology & Biochemistry , University of Bath , Bath BA2 7AY , U.K
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Lu T, Zou Y, Xu G, Potter JA, Taylor GL, Duan Q, Yang Q, Xiong H, Qiu H, Ye D, Zhang P, Yu S, Yuan X, Zhu F, Wang Y, Xiong H. PRIMA-1Met suppresses colorectal cancer independent of p53 by targeting MEK. Oncotarget 2018; 7:83017-83030. [PMID: 27806324 PMCID: PMC5347749 DOI: 10.18632/oncotarget.12940] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 10/10/2016] [Indexed: 01/06/2023] Open
Abstract
PRIMA-1Met is the methylated PRIMA-1 (p53 reactivation and induction of massive apoptosis) and could restore tumor suppressor function of mutant p53 and induce p53 dependent apoptosis in cancer cells harboring mutant p53. However, p53 independent activity of PRIMA-1Met remains elusive. Here we reported that PRIMA-1Met attenuated colorectal cancer cell growth irrespective of p53 status. Kinase profiling revealed that mitogen-activated or extracellular signal-related protein kinase (MEK) might be a potential target of PRIMA-1Met. Pull-down binding and ATP competitive assay showed that PRIMA-1Met directly bound MEK in vitro and in cells. Furthermore, the direct binding sites of PRIMA-1Met were explored by using a computational docking model. Treatment of colorectal cancer cells with PRIMA-1Met inhibited p53-independent phosphorylation of MEK, which in turn impaired anchorage-independent cell growth in vitro. Moreover, PRIMA-1Met suppressed colorectal cancer growth in xenograft mouse model by inhibiting MEK1 activity. Taken together, our findings demonstrate a novel p53-independent activity of PRIMA-1Met to inhibit MEK and suppress colorectal cancer growth.
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Affiliation(s)
- Tao Lu
- Department of Biochemistry and molecular biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanmei Zou
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Guogang Xu
- Nanlou Respiratory Department, Chinese PLA General Hospital, Beijing, 10083, China
| | - Jane A Potter
- BioMedical Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Garry L Taylor
- BioMedical Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Qiuhong Duan
- Department of Biochemistry and molecular biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qin Yang
- Department of Pathology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hong Qiu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dawei Ye
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shiying Yu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Feng Zhu
- Department of Biochemistry and molecular biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yihua Wang
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China
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Yang L, Connaris H, Potter JA, Taylor GL. Erratum to: Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor. BMC Struct Biol 2015; 15:19. [PMID: 26444866 PMCID: PMC4596311 DOI: 10.1186/s12900-015-0047-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/01/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Lei Yang
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, Fife, UK
| | - Helen Connaris
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, Fife, UK.
| | - Jane A Potter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, Fife, UK
| | - Garry L Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, Fife, UK
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Owen CD, Lukacik P, Potter JA, Sleator O, Taylor GL, Walsh MA. Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR. J Biol Chem 2015; 290:27736-48. [PMID: 26370075 PMCID: PMC4646021 DOI: 10.1074/jbc.m115.673632] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 06/29/2015] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen that causes a range of disease states. Sialidases are important bacterial virulence factors. There are three pneumococcal sialidases: NanA, NanB, and NanC. NanC is an unusual sialidase in that its primary reaction product is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en, also known as DANA), a nonspecific hydrolytic sialidase inhibitor. The production of Neu5Ac2en from α2–3-linked sialosides by the catalytic domain is confirmed within a crystal structure. A covalent complex with 3-fluoro-β-N-acetylneuraminic acid is also presented, suggesting a common mechanism with other sialidases up to the final step of product formation. A conformation change in an active site hydrophobic loop on ligand binding constricts the entrance to the active site. In addition, the distance between the catalytic acid/base (Asp-315) and the ligand anomeric carbon is unusually short. These features facilitate a novel sialidase reaction in which the final step of product formation is direct abstraction of the C3 proton by the active site aspartic acid, forming Neu5Ac2en. NanC also possesses a carbohydrate-binding module, which is shown to bind α2–3- and α2–6-linked sialosides, as well as N-acetylneuraminic acid, which is captured in the crystal structure following hydration of Neu5Ac2en by NanC. Overall, the pneumococcal sialidases show remarkable mechanistic diversity while maintaining a common structural scaffold.
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Affiliation(s)
- C David Owen
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Petra Lukacik
- Diamond Light Source and Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom, and
| | - Jane A Potter
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Olivia Sleator
- the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Garry L Taylor
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom,
| | - Martin A Walsh
- Diamond Light Source and the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
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Yang L, Connaris H, Potter JA, Taylor GL. Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor. BMC Struct Biol 2015; 15:15. [PMID: 26289431 PMCID: PMC4546082 DOI: 10.1186/s12900-015-0042-4] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/11/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Streptococcus pneumoniae Neuraminidase A (NanA) is a multi-domain protein anchored to the bacterial surface. Upstream of the catalytic domain of NanA is a domain that conforms to the sialic acid-recognising CBM40 family of the CAZY (carbohydrate-active enzymes) database. This domain has been identified to play a critical role in allowing the bacterium to promote adhesion and invasion of human brain microvascular endothelial cells, and hence may play a key role in promoting bacterial meningitis. In addition, the CBM40 domain has also been reported to activate host chemokines and neutrophil recruitment during infection. RESULTS Crystal structures of both apo- and holo- forms of the NanA CBM40 domain (residues 121 to 305), have been determined to 1.8 Å resolution. The domain shares the fold of other CBM40 domains that are associated with sialidases. When in complex with α2,3- or α2,6-sialyllactose, the domain is shown to interact only with the terminal sialic acid. Significantly, a deep acidic pocket adjacent to the sialic acid-binding site is identified, which is occupied by a lysine from a symmetry-related molecule in the crystal. This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions. CONCLUSIONS The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface. The structure also suggests that small molecules or sialic acid analogues could be developed to fill the acidic pocket and hence provide a new therapeutic avenue against meningitis caused by S. pneumoniae.
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Affiliation(s)
- Lei Yang
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
| | - Helen Connaris
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
| | - Jane A Potter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
| | - Garry L Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
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Yeung JHF, Telford JC, Shidmoossavee FS, Bennet AJ, Taylor GL, Moore MM. Kinetic and Structural Evaluation of Selected Active Site Mutants of the Aspergillus fumigatus KDNase (Sialidase). Biochemistry 2013; 52:9177-86. [DOI: 10.1021/bi401166f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | | | | | | | - Garry L. Taylor
- BSRC, University of St Andrews, St Andrews, Fife KY16 9ST, U.K
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Brear P, Telford J, Taylor GL, Westwood NJ. Synthesis and Structural Characterisation of Selective Non-Carbohydrate-Based Inhibitors of Bacterial Sialidases. Chembiochem 2012; 13:2374-83. [DOI: 10.1002/cbic.201200433] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Indexed: 11/08/2022]
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Hayre JK, Xu G, Borgianni L, Taylor GL, Andrew PW, Docquier JD, Oggioni MR. Optimization of a direct spectrophotometric method to investigate the kinetics and inhibition of sialidases. BMC Biochem 2012; 13:19. [PMID: 23031230 PMCID: PMC3483245 DOI: 10.1186/1471-2091-13-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 09/25/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUNDS Streptococcus pneumoniae expresses three distinct sialidases, NanA, NanB, and NanC, that are believed to be key virulence factors and thus, potential important drug targets. We previously reported that the three enzymes release different products from sialosides, but could share a common catalytic mechanism before the final step of product formation. However, the kinetic investigations of the three sialidases have not been systematically done thus far, due to the lack of an easy and steady measurement of sialidase reaction rate. RESULTS In this work, we present further kinetic characterization of pneumococcal sialidases by using a direct spectrophotometric method with the chromogenic substrate p-nitrophenyl-N-acetylneuraminic acid (p-NP-Neu5Ac). Using our assay, the measured kinetic parameters of the three purified pneumococcal sialidase, NanA, NanB and NanC, were obtained and were in perfect agreement with the previously published data. The major advantage of this alternative method resides in the direct measurement of the released product, allowing to readily determine of initial reaction rates and record complete hydrolysis time courses. CONCLUSION We developed an accurate, fast and sensitive spectrophotometric method to investigate the kinetics of sialidase-catalyzed reactions. This fast, sensitive, inexpensive and accurate method could benefit the study of the kinetics and inhibition of sialidases in general.
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Affiliation(s)
- Jasvinder Kaur Hayre
- Dipartimento di Biotecnologie, Università degli Studi di Siena, I-53100, Siena, Italy
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Alymova IV, Portner A, Mishin VP, McCullers JA, Freiden P, Taylor GL. Receptor-binding specificity of the human parainfluenza virus type 1 hemagglutinin-neuraminidase glycoprotein. Glycobiology 2011; 22:174-80. [PMID: 21846691 DOI: 10.1093/glycob/cwr112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The hemagglutinin-neuraminidase (HN) glycoprotein is utilized by human parainfluenza viruses for binding to the host cell. By the use of glycan array assays, we demonstrate that, in addition to the first catalytic-binding site, the HN of human parainfluenza virus type 1 has a second site for binding covered by N-linked glycan. Our data suggest that attachment of the first site to sialic acid (SA)-linked receptors triggers exposure of the second site. We found that both sites bind to α2-3-linked SAs with a preference for a sialyl-Lewis(x) motif. Binding to α2-3-linked SAs with a sulfated sialyl-Lewis motif as well as to α2-8-linked SAs was unique for the second binding site. Neither site recognizes α2-6-linked oligosaccharides.
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Affiliation(s)
- Irina V Alymova
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA.
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Gut H, Xu G, Taylor GL, Walsh MA. Structural Basis for Streptococcus pneumoniae NanA Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate. J Mol Biol 2011; 409:496-503. [DOI: 10.1016/j.jmb.2011.04.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/27/2022]
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Telford JC, Yeung JHF, Xu G, Kiefel MJ, Watts AG, Hader S, Chan J, Bennet AJ, Moore MM, Taylor GL. The Aspergillus fumigatus sialidase is a 3-deoxy-D-glycero-D-galacto-2-nonulosonic acid hydrolase (KDNase): structural and mechanistic insights. J Biol Chem 2011; 286:10783-92. [PMID: 21247893 DOI: 10.1074/jbc.m110.207043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aspergillus fumigatus is a filamentous fungus that can cause severe respiratory disease in immunocompromised individuals. A putative sialidase from A. fumigatus was recently cloned and shown to be relatively poor in cleaving N-acetylneuraminic acid (Neu5Ac) in comparison with bacterial sialidases. Here we present the first crystal structure of a fungal sialidase. When the apo structure was compared with bacterial sialidase structures, the active site of the Aspergillus enzyme suggested that Neu5Ac would be a poor substrate because of a smaller pocket that normally accommodates the acetamido group of Neu5Ac in sialidases. A sialic acid with a hydroxyl in place of an acetamido group is 2-keto-3-deoxynononic acid (KDN). We show that KDN is the preferred substrate for the A. fumigatus sialidase and that A. fumigatus can utilize KDN as a sole carbon source. A 1.45-Å resolution crystal structure of the enzyme in complex with KDN reveals KDN in the active site in a boat conformation and nearby a second binding site occupied by KDN in a chair conformation, suggesting that polyKDN may be a natural substrate. The enzyme is not inhibited by the sialidase transition state analog 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (Neu5Ac2en) but is inhibited by the related 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid that we show bound to the enzyme in a 1.84-Å resolution crystal structure. Using a fluorinated KDN substrate, we present a 1.5-Å resolution structure of a covalently bound catalytic intermediate. The A. fumigatus sialidase is therefore a KDNase with a similar catalytic mechanism to Neu5Ac exosialidases, and this study represents the first structure of a KDNase.
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Affiliation(s)
- Judith C Telford
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
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Xu G, Kiefel MJ, Wilson JC, Andrew PW, Oggioni MR, Taylor GL. Three Streptococcus pneumoniae sialidases: three different products. J Am Chem Soc 2011; 133:1718-21. [PMID: 21244006 DOI: 10.1021/ja110733q] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Streptococcus penumoniae is a major human pathogen responsible for respiratory tract infections, septicemia, and meningitis and continues to produce numerous cases of disease with relatively high mortalities. S. pneumoniae encodes up to three sialidases, NanA, NanB, and NanC, that have been implicated in pathogenesis and are potential drug targets. NanA has been shown to be a promiscuous sialidase, hydrolyzing the removal of Neu5Ac from a variety of glycoconjugates with retention of configuration at the anomeric center, as we confirm by NMR. NanB is an intramolecular trans-sialidase producing 2,7-anhydro-Neu5Ac selectively from α2,3-sialosides. Here, we show that the first product of NanC is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en) that can be slowly hydrated by the enzyme to Neu5Ac. We propose that the three pneumococcal sialidases share a common catalytic mechanism up to the final product formation step, and speculate on the roles of the enzymes in the lifecycle of the bacterium.
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Affiliation(s)
- Guogang Xu
- Biomedical Sciences Research Complex, University of St. Andrews, KY16 9ST, UK
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Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CAJ, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DTF, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH. The Scottish Structural Proteomics Facility: targets, methods and outputs. ACTA ACUST UNITED AC 2010; 11:167-80. [PMID: 20419351 PMCID: PMC2883930 DOI: 10.1007/s10969-010-9090-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 12/19/2022]
Abstract
The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
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Affiliation(s)
- Muse Oke
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Lester G. Carter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Stanford Synchrotron Radiation Light Source, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025 USA
| | - Kenneth A. Johnson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Xuan Yan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Melina Kerou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Nadine D. Weikart
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Faculty of Chemistry, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- Present Address: Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG UK
| | - Md. Arif Sheikh
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stefan Schmelz
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Mark Dorward
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Division of Signal Transduction Therapy, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Michal Zawadzki
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, RG42 6EY UK
| | - Christopher Cozens
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Helen Falconer
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Institute of Structural and Molecular Biology, Edinburgh University, Kings Buildings, Edinburgh, EH9 3JR UK
| | - Helen Powers
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Ian M. Overton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
- Present Address: MRC Human Genetics Unit, Crewe Road South, Edinburgh, EH4 2XU UK
| | - C. A. Johannes van Niekerk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Xu Peng
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Prakash Patel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Roger A. Garrett
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Peter J. Coote
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - David T. F. Dryden
- EaStChem School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JJ UK
| | - Geoffrey J. Barton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | | | - Garry L. Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
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20
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Abstract
When collecting X-ray diffraction data from a crystal, we measure the intensities of the diffracted waves scattered from a series of planes that we can imagine slicing through the crystal in all directions. From these intensities we derive the amplitudes of the scattered waves, but in the experiment we lose the phase information; that is, how we offset these waves when we add them together to reconstruct an image of our molecule. This is generally known as the 'phase problem'. We can only derive the phases from some knowledge of the molecular structure. In small-molecule crystallography, some basic assumptions about atomicity give rise to relationships between the amplitudes from which phase information can be extracted. In protein crystallography, these ab initio methods can only be used in the rare cases in which there are data to at least 1.2 A resolution. For the majority of cases in protein crystallography phases are derived either by using the atomic coordinates of a structurally similar protein (molecular replacement) or by finding the positions of heavy atoms that are intrinsic to the protein or that have been added (methods such as MIR, MIRAS, SIR, SIRAS, MAD, SAD or combinations of these). The pioneering work of Perutz, Kendrew, Blow, Crick and others developed the methods of isomorphous replacement: adding electron-dense atoms to the protein without disturbing the protein structure. Nowadays, methods from small-molecule crystallography can be used to find the heavy-atom substructure and the phases for the whole protein can be bootstrapped from this prior knowledge. More recently, improved X-ray sources, detectors and software have led to the routine use of anomalous scattering to obtain phase information from either incorporated selenium or intrinsic sulfurs. In the best cases, only a single set of X-ray data (SAD) is required to provide the positions of the anomalous scatters, which together with density-modification procedures can reveal the structure of the complete protein.
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Affiliation(s)
- Garry L Taylor
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland.
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21
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Jahan N, Potter JA, Sheikh MA, Botting CH, Shirran SL, Westwood NJ, Taylor GL. Erratum to “Insights into the Biosynthesis of the Vibrio cholera Major Autoinducer CAI-1 from the Crystal Structure of the PLP-Dependent Enzyme CqsA” [J. Mol. Biol. (2009) 92, 763–773]. J Mol Biol 2009. [DOI: 10.1016/j.jmb.2009.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Jahan N, Potter JA, Sheikh MA, Botting CH, Shirran SL, Westwood NJ, Taylor GL. Insights into the Biosynthesis of the Vibrio cholerae Major Autoinducer CAI-1 from the Crystal Structure of the PLP-Dependent Enzyme CqsA. J Mol Biol 2009; 392:763-73. [DOI: 10.1016/j.jmb.2009.07.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/12/2009] [Accepted: 07/14/2009] [Indexed: 10/20/2022]
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23
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Abstract
The ferric uptake regulator (Fur) is a metal-dependent DNA-binding protein that acts as both a repressor and an activator of numerous genes involved in maintaining iron homeostasis in bacteria. It has also been demonstrated in Vibrio cholerae that Fur plays an additional role in pathogenesis, opening up the potential of Fur as a drug target for cholera. Here we present the crystal structure of V. cholerae Fur that reveals a very different orientation of the DNA-binding domains compared with that observed in Pseudomonas aeruginosa Fur. Each monomer of the dimeric Fur protein contains two metal binding sites occupied by zinc in the crystal structure. In the P. aeruginosa study these were designated as the regulatory site (Zn1) and structural site (Zn2). This V. cholerae Fur study, together with studies on Fur homologues and paralogues, suggests that in fact the Zn2 site is the regulatory iron binding site and the Zn1 site plays an auxiliary role. There is no evidence of metal binding to the cysteines that are conserved in many Fur homologues, including Escherichia coli Fur. An analysis of the metal binding properties shows that V. cholerae Fur can be activated by a range of divalent metals.
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Affiliation(s)
- Md Arif Sheikh
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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24
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Xu G, Ryan C, Kiefel MJ, Wilson JC, Taylor GL. Structural Studies on the Pseudomonas aeruginosa Sialidase-Like Enzyme PA2794 Suggest Substrate and Mechanistic Variations. J Mol Biol 2009; 386:828-40. [DOI: 10.1016/j.jmb.2008.12.084] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/23/2008] [Accepted: 12/31/2008] [Indexed: 12/01/2022]
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25
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Connaris H, Crocker PR, Taylor GL. Enhancing the receptor affinity of the sialic acid-binding domain of Vibrio cholerae sialidase through multivalency. J Biol Chem 2009; 284:7339-51. [PMID: 19124471 DOI: 10.1074/jbc.m807398200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many glycoside hydrolases possess carbohydrate-binding modules (CBMs) that help target these enzymes to appropriate substrates and increase their catalytic efficiency. The Vibrio cholerae sialidase contains two CBMs, one of which is designated as a family CBM40 module and has been shown through structural and calorimetry studies to recognize the alpha-anomer of sialic acid with a KD of approximately 30 microM at 37 degrees C. The affinity of this V. cholerae CBM40 module for sialic acid is one of the highest reported for recognition of a monosaccharide by a CBM. As Nature often increases a weak substrate affinity through multivalency, we have explored the potential of developing reagents with an increased affinity for sialic acid receptors through linking CBM40 modules together. The V. cholerae CBM40 was subcloned and crystallized in the presence of sialyllactose confirming its ability to recognize sialic acid. Calorimetry revealed that this CBM40 demonstrated specificity to alpha(2,3)-, alpha(2,6)-, and alpha(2,8)-linked sialosides. Polypeptides containing up to four CBM40 modules in tandem were created to determine if an increase in affinity to sialic acid could be achieved through an avidity effect. Using SPR and a multivalent alpha(2,3)-sialyllactose ligand, we show that increasing the number of linked modules does increase the affinity for sialic acid. The four-CBM40 module protein has a 700- to 1500-fold increase in affinity compared with the single-CBM40 module. Varying the linker length of amino acids between each CBM40 module had little effect on the binding of these polypeptides. Finally, fluorescence-activated cell sorting analysis demonstrated that a green fluorescent protein fused to three CBM40 modules bound to subpopulations of human leukocytes. These studies lay the foundation for creating high affinity, multivalent CBMs that could have broad application in glycobiology.
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Affiliation(s)
- Helen Connaris
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK.
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26
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Xu G, Potter JA, Russell RJ, Oggioni MR, Andrew PW, Taylor GL. Crystal Structure of the NanB Sialidase from Streptococcus pneumoniae. J Mol Biol 2008; 384:436-49. [DOI: 10.1016/j.jmb.2008.09.032] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 09/07/2008] [Accepted: 09/12/2008] [Indexed: 11/26/2022]
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Potter JA, Kerou M, Lamble HJ, Bull SD, Hough DW, Danson MJ, Taylor GL. The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase. Acta Crystallogr D Biol Crystallogr 2008; 64:1283-7. [PMID: 19018105 DOI: 10.1107/s0907444908036111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 11/04/2008] [Indexed: 11/10/2022]
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 353 K and utilizes an unusual promiscuous nonphosphorylative Entner-Doudoroff pathway to metabolize both glucose and galactose. It has been proposed that a part-phosphorylative Entner-Doudoroff pathway occurs in parallel in S. solfataricus, in which the 2-keto-3-deoxygluconate kinase (KDGK) is promiscuous for both glucose and galactose metabolism. Recombinant S. solfataricus KDGK protein was expressed in Escherichia coli, purified and crystallized in 0.1 M sodium acetate pH 4.1 and 1.4 M NaCl. The crystal structure of apo S. solfataricus KDGK was solved by molecular replacement to a resolution of 2.0 A and a ternary complex with 2-keto-3-deoxygluconate (KDGlu) and an ATP analogue was resolved at 2.1 A. The complex suggests that the structural basis for the enzyme's ability to phosphorylate KDGlu and 2-keto-3-deoxygalactonate (KDGal) is derived from a subtle repositioning of residues that are conserved in homologous nonpromiscuous kinases.
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Affiliation(s)
- Jane A Potter
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
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28
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Xu G, Li X, Andrew PW, Taylor GL. Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:772-5. [PMID: 18765901 PMCID: PMC2531273 DOI: 10.1107/s1744309108024044] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 07/29/2008] [Indexed: 11/15/2022]
Abstract
Streptococcus pneumoniae genomes encode three sialidases, NanA, NanB and NanC, which are key virulence factors that remove sialic acids from various glycoconjugates. The enzymes have potential as drug targets and also as vaccine candidates. The 115 kDa NanA is the largest of the three sialidases and is anchored to the bacterial membrane. Although recombinantly expressed full-length NanA was soluble, it failed to crystallize; therefore, a 56.5 kDa domain that retained full enzyme activity was subcloned. The purified enzyme was crystallized in 0.1 M MES pH 6.5, 30%(w/v) PEG 4000 using the sitting-drop vapour-diffusion method. Data were collected at 100 K to 2.5 A resolution from a crystal grown in the presence of the inhibitor 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 49.2, b = 95.6, c = 226.6 A. The structure was solved by molecular replacement and refined to final R and R(free) factors of 0.246 and 0.298, respectively.
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Affiliation(s)
- Guogang Xu
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland
| | - Xuejun Li
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland
| | - Peter W. Andrew
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, England
| | - Garry L. Taylor
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland
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29
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Sheikh MA, Potter JA, Johnson KA, Sim RB, Boyd EF, Taylor GL. Crystal structure of VC1805, a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to human p32. Proteins 2008; 71:1563-71. [PMID: 18300248 DOI: 10.1002/prot.21993] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Md Arif Sheikh
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife, KY16 9ST, United Kingdom
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30
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Taylor GL, Murphy NF, Berry C, Christie J, Finlayson A, MacIntyre K, Morrison C, McMurray J. Long-term outcome of low-risk patients attending a rapid-assessment chest pain clinic. Heart 2008; 94:628-32. [DOI: 10.1136/hrt.2007.125344] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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31
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Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL. The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. J Biol Chem 2008; 283:9080-8. [PMID: 18218621 PMCID: PMC2431023 DOI: 10.1074/jbc.m710247200] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [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: 12/17/2007] [Revised: 01/10/2008] [Indexed: 11/06/2022] Open
Abstract
Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.
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Affiliation(s)
- Simon L Newstead
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Fife, United Kingdom
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32
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Potter JA, Randall RE, Taylor GL. Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain. BMC Struct Biol 2008; 8:11. [PMID: 18307765 PMCID: PMC2291057 DOI: 10.1186/1472-6807-8-11] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 02/28/2008] [Indexed: 12/24/2022]
Abstract
Background IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral response two RNA helicases, retinoic acid inducible gene-I (RIG-I) and melanoma differentiation-association gene 5 (MDA5), are independently able to bind viral RNA in the cytoplasm. The 62 kDa protein IPS-1/MAVS/VISA/Cardif contains an N-terminal caspase activation and recruitment (CARD) domain that associates with the CARD regions of RIG-I and MDA5, ultimately leading to the induction of type I interferons. As a first step towards understanding the molecular basis of this important adaptor protein we have undertaken structural studies of the IPS-1 MAVS/VISA/Cardif CARD region. Results The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1Å resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion protein. The MBP and IPS-1 components each form a distinct domain within the structure. IPS-1/MAVS/VISA/Cardif CARD adopts a characteristic six-helix bundle with a Greek-key topology and, in common with a number of other known CARD structures, contains two major polar surfaces on opposite sides of the molecule. One face has a surface-exposed, disordered tryptophan residue that may explain the poor solubility of untagged expression constructs. Conclusion The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein interactions. The location of the two polar areas on IPS-1/MAVS/VISA/Cardif CARD suggest possible types of associations that this domain makes with the two CARD domains of MDA5 or RIG-I. The N-terminal CARD domains of RIG-I and MDA5 share greatest sequence similarity with IPS-1/MAVS/VISA/Cardif CARD and this has allowed modelling of their structures. These models show a very different charge profile for the equivalent surfaces compared to IPS-1/MAVS/VISA/Cardif CARD.
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Affiliation(s)
- Jane A Potter
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
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33
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Seetharamappa J, Oke M, Liu H, McMahon SA, Johnson KA, Carter L, Dorward M, Zawadzki M, Overton IM, van Niekirk CAJ, Graham S, Botting CH, Taylor GL, White MF, Barton GJ, Coote PJ, Naismith JH. Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:488-91. [PMID: 17554169 PMCID: PMC2335074 DOI: 10.1107/s1744309107020362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 03/25/2007] [Accepted: 04/24/2007] [Indexed: 11/10/2022]
Abstract
Sar2676, a pantothenate synthetase with a molecular weight of 31 419 Da from methicillin-resistant Staphylococcus aureus, has been expressed, purified and crystallized at 293 K. The protein crystallizes in a primitive triclinic lattice, with unit-cell parameters a = 45.3, b = 60.5, c = 117.6 A, alpha = 87.2, beta = 81.2, gamma = 68.4 degrees . A complete data set has been collected to 2.3 A resolution at the ESRF. Consideration of the likely solvent content suggested the asymmetric unit to contain four molecules. This has been confirmed by molecular-replacement phasing calculations, which give a solution with four monomers using a monomer of pantothenate synthetase from Escherichia coli (PDB code 1iho), which is 41% identical to Sar2676, as a search model.
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Affiliation(s)
- Jaldappagari Seetharamappa
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
- Department of Chemistry, Karnatak University, Pavate Nagar, Dharwad 580 003, Karnataka State, India
| | - Muse Oke
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Huanting Liu
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Stephen A. McMahon
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Kenneth A. Johnson
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Lester Carter
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Mark Dorward
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Michal Zawadzki
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Ian M. Overton
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - C. A. Johannes van Niekirk
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Shirley Graham
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Catherine H. Botting
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Garry L. Taylor
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Malcolm F. White
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Geoffrey J. Barton
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Peter J. Coote
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - James H. Naismith
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
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34
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Abstract
N-terminal protein acetylation is common in eukaryotes and halophilic archaea, but very rare in bacteria. We demonstrate that some of the most abundant proteins present in the crenarchaeote Sulfolobus solfataricus, including subunits of the thermosome, proteosome and ribosome, are acetylated at the N-terminus. Modification was observed at the N-terminal residues serine, alanine, threonine and methionine-glutamate. A conserved archaeal protein, ssArd1, was cloned and expressed in Escherichia coli, and shown to acetylate the same N-terminal sequences in vitro. The specific activity of ssArd1 is sensitive to protein structure in addition to sequence context. The crenarchaeota and euryarchaeota apparently differ in respect of the frequency of acetylation of Met-Glu termini, which appears much more common in S. solfataricus. This sequence is acetylated by the related Nat3 acetylase in eukarya. ssArd1 thus has a relaxed sequence specificity compared with the eukaryotic N-acetyl transferases, and may represent an ancestral form of the enzyme. This represents another example where archaeal molecular biology resembles that in eukaryotes rather than bacteria.
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Affiliation(s)
- Dale T Mackay
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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35
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Seetharamappa J, Oke M, Liu H, McMahon SA, Johnson KA, Carter L, Dorward M, Zawadzki M, Overton IM, van Niekirk CAJ, Graham S, Botting CH, Taylor GL, White MF, Barton GJ, Coote PJ, Naismith JH. Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:452-6. [PMID: 17565195 PMCID: PMC2335000 DOI: 10.1107/s1744309107019562] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 03/22/2007] [Accepted: 04/19/2007] [Indexed: 11/10/2022]
Abstract
Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase with a molecular weight of 48,168 Da, was overexpressed in methicillin-resistant Staphylococcus aureus compared with a methicillin-sensitive strain. The protein was expressed in Escherichia coli, purified and crystallized. The protein crystallized in a primitive orthorhombic Laue group with unit-cell parameters a = 83.6, b = 91.3, c = 106.0 A, alpha = beta = gamma = 90 degrees. Analysis of the systematic absences along the three principal axes indicated the space group to be P2(1)2(1)2(1). A complete data set was collected to 2.5 A resolution.
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Affiliation(s)
- Jaldappagari Seetharamappa
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
- Department of Chemistry, Karnatak University, Pavate Nagar, Dharwad 580 003, Karnataka State, India
| | - Muse Oke
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Huanting Liu
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Stephen A. McMahon
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Kenneth A. Johnson
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Lester Carter
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Mark Dorward
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Michal Zawadzki
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Ian M. Overton
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - C. A. Johannes van Niekirk
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Shirley Graham
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Catherine H. Botting
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Garry L. Taylor
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Malcolm F. White
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - Geoffrey J. Barton
- Scottish Structural Facility and School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Peter J. Coote
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
| | - James H. Naismith
- Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
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McMahon SA, Walsh MA, Ching RTY, Carter LG, Dorward M, Johnson KA, Liu H, Oke M, Bloch C, Kennedy MW, Latiff AA, Cooper A, Taylor GL, White MF, Naismith JH. Crystallization of Ranasmurfin, a blue-coloured protein from Polypedates leucomystax. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1124-6. [PMID: 17077494 PMCID: PMC2225219 DOI: 10.1107/s1744309106040036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 09/29/2006] [Indexed: 05/12/2023]
Abstract
Ranasmurfin, a previously uncharacterized approximately 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 A with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 A, beta = 93.3 degrees . Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution.
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Affiliation(s)
- Stephen A. McMahon
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Martin A. Walsh
- Medical Research Council France, European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX, France
| | - Rosalind Tan Yan Ching
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
- Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Lester G. Carter
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Mark Dorward
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Kenneth A. Johnson
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Huanting Liu
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Muse Oke
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Carlos Bloch
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Asa Norte, Brasilia 70910-900, Brazil
| | - Malcolm W. Kennedy
- Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Aishah A. Latiff
- Doping Control Centre Penang, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Alan Cooper
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Garry L. Taylor
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - Malcolm F. White
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
| | - James H. Naismith
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland
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37
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Kukowski AC, Maddock RJ, Wulf DM, Fausti SW, Taylor GL. Evaluating consumer acceptability and willingness to pay for various beef chuck muscles. J Anim Sci 2006; 83:2605-10. [PMID: 16230658 DOI: 10.2527/2005.83112605x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In-home consumer steak evaluations, followed by centralized laboratory-setting auctions, were used to determine consumer (n = 74 consumers) acceptability and willingness to pay for various beef chuck muscles. The infraspinatus (IF), serratus ventralis (SV), supraspinatus (SS), and triceps brachii (TB) from the beef chuck were evaluated against LM steaks from the rib to determine price and trait differentials. Muscles from USDA Choice, boneless, boxed-beef sub-primals were aged 14 d, frozen, and cut into 2.5-cm-thick steaks. Consumers received two steaks from each muscle for in-home evaluations of uncooked steak appearance and cooked steak palatability. After in-home evaluation of steaks, consumers participated in a random nth price auction session to determine willingness to pay for those steaks. Muscles differed (P < 0.05) for overall like of appearance, like of size, like of shape, and like of leanness; LM generally rated the highest. Steaks from the LM rated highest (P < 0.05) for overall like, and steaks from the SS and SV were lowest (P < 0.05) for overall like. Juiciness and beef flavor intensity scores were highest (P < 0.05) for steaks from the LM and IF, whereas SS steaks received the lowest (P < 0.05) juiciness scores, and SS and SV steaks were rated lowest (P < 0.05) for beef flavor intensity. Average auction price differentials differed (P < 0.05) from the LM, and were -0.71 dollars, -0.79 dollars, -1.75 dollars, and -2.44 dollars/0.45 kg for the TB, IF, SS, and SV, respectively. Average appearance trait differentials and average palatability trait differentials were correlated significantly with average price differentials. Results indicate the IF and TB were acceptable to consumers as steaks but only at prices lower than the LM.
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Affiliation(s)
- A C Kukowski
- Department of Animal and Range Science, South Dakota State University, Brookings, 57007, USA
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38
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Williams GJ, Johnson K, Rudolf J, McMahon SA, Carter L, Oke M, Liu H, Taylor GL, White MF, Naismith JH. Structure of the heterotrimeric PCNA from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:944-8. [PMID: 17012780 PMCID: PMC2225174 DOI: 10.1107/s1744309106034075] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [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: 07/06/2006] [Accepted: 08/24/2006] [Indexed: 11/10/2022]
Abstract
PCNA is a ring-shaped protein that encircles DNA, providing a platform for the association of a wide variety of DNA-processing enzymes that utilize the PCNA sliding clamp to maintain proximity to their DNA substrates. PCNA is a homotrimer in eukaryotes, but a heterotrimer in crenarchaea such as Sulfolobus solfataricus. The three proteins are SsoPCNA1 (249 residues), SsoPCNA2 (245 residues) and SsoPCNA3 (259 residues). The heterotrimeric protein crystallizes in space group P2(1), with unit-cell parameters a = 44.8, b = 78.8, c = 125.6 A, beta = 100.5 degrees. The crystal structure of this heterotrimeric PCNA molecule has been solved using molecular replacement. The resulting structure to 2.3 A sheds light on the differential stabilities of the interactions observed between the three subunits and the specificity of individual subunits for partner proteins.
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Affiliation(s)
- Gareth J. Williams
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Kenneth Johnson
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Jana Rudolf
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Stephen A. McMahon
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Lester Carter
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Muse Oke
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Huanting Liu
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Garry L. Taylor
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - Malcolm F. White
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
| | - James H. Naismith
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews, Fife KY16 9RH, Scotland
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39
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Milburn CC, Lamble HJ, Theodossis A, Bull SD, Hough DW, Danson MJ, Taylor GL. The Structural Basis of Substrate Promiscuity in Glucose Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus solfataricus. J Biol Chem 2006; 281:14796-804. [PMID: 16556607 DOI: 10.1074/jbc.m601334200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 80 degrees C and utilizes an unusual, promiscuous, non-phosphorylative Entner-Doudoroff pathway to metabolize both glucose and galactose. The first enzyme in this pathway, glucose dehydrogenase, catalyzes the oxidation of glucose to gluconate, but has been shown to have activity with a broad range of sugar substrates, including glucose, galactose, xylose, and L-arabinose, with a requirement for the glucose stereo configuration at the C2 and C3 positions. Here we report the crystal structure of the apo form of glucose dehydrogenase to a resolution of 1.8 A and a complex with its required cofactor, NADP+, to a resolution of 2.3 A. A T41A mutation was engineered to enable the trapping of substrate in the crystal. Complexes of the enzyme with D-glucose and D-xylose are presented to resolutions of 1.6 and 1.5 A, respectively, that provide evidence of selectivity for the beta-anomeric, pyranose form of the substrate, and indicate that this is the productive substrate form. The nature of the promiscuity of glucose dehydrogenase is also elucidated, and a physiological role for this enzyme in xylose metabolism is suggested. Finally, the structure suggests that the mechanism of sugar oxidation by this enzyme may be similar to that described for human sorbitol dehydrogenase.
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Affiliation(s)
- Christine C Milburn
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, Scotland, UK
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Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 2005; 579:6865-9. [PMID: 16330030 DOI: 10.1016/j.febslet.2005.11.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [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: 09/19/2005] [Revised: 11/03/2005] [Accepted: 11/03/2005] [Indexed: 11/25/2022]
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus metabolises glucose and galactose by a 'promiscuous' non-phosphorylative variant of the Entner-Doudoroff pathway, in which a series of enzymes have sufficient substrate promiscuity to permit the metabolism of both sugars. Recently, it has been proposed that the part-phosphorylative Entner-Doudoroff pathway occurs in parallel in S. solfataricus as an alternative route for glucose metabolism. In this report we demonstrate, by in vitro kinetic studies of D-2-keto-3-deoxygluconate (KDG) kinase and KDG aldolase, that the part-phosphorylative pathway in S. solfataricus is also promiscuous for the metabolism of both glucose and galactose.
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Affiliation(s)
- Henry J Lamble
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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41
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Jelinska C, Conroy MJ, Craven CJ, Hounslow AM, Bullough PA, Waltho JP, Taylor GL, White MF. Obligate Heterodimerization of the Archaeal Alba2 Protein with Alba1 Provides a Mechanism for Control of DNA Packaging. Structure 2005; 13:963-71. [PMID: 16004869 DOI: 10.1016/j.str.2005.04.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [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: 03/22/2005] [Revised: 04/23/2005] [Accepted: 04/23/2005] [Indexed: 11/16/2022]
Abstract
Organisms growing at elevated temperatures face a particular challenge to maintain the integrity of their genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of the Alba (Sac10b) gene. Alba is an abundant, dimeric, highly basic protein that binds cooperatively and at high density to DNA. Sulfolobus solfataricus encodes a second copy of the Alba gene, and the Alba2 protein is expressed at approximately 5% of the level of Alba1. We demonstrate by NMR, ITC, and crystallography that Alba2 exists exclusively as a heterodimer with Alba1 at physiological concentrations and that heterodimerization exerts a clear effect upon the DNA packaging, as observed by EM, potentially by changing the interface between adjacent Alba dimers in DNA complexes. A functional role for Alba2 in modulation of higher order chromatin structure and DNA condensation is suggested.
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Affiliation(s)
- Clare Jelinska
- Centre for Biomolecular Science, University of Saint Andrews, North Haugh, Saint Andrews, Fife KY16 9ST, United Kingdom
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42
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Theodossis A, Milburn CC, Heyer NI, Lamble HJ, Hough DW, Danson MJ, Taylor GL. Preliminary crystallographic studies of glucose dehydrogenase from the promiscuous Entner-Doudoroff pathway in the hyperthermophilic archaeon Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:112-5. [PMID: 16508107 PMCID: PMC1952374 DOI: 10.1107/s174430910403101x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 11/25/2004] [Indexed: 11/10/2022]
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 353 K and can metabolize glucose and its C4 epimer galactose via a non-phosphorylative variant of the Entner-Doudoroff pathway involving catalytically promiscuous enzymes that can operate with both sugars. The initial oxidation step is catalysed by glucose dehydrogenase (SsGDH), which can utilize both NAD and NADP as cofactors. The enzyme operates with glucose and galactose at similar catalytic efficiency, while its substrate profile also includes a range of other five- and six-carbon sugars. Crystals of the 164 kDa SsGDH homotetramer have been grown under a variety of conditions. The best crystals to date diffract to 1.8 A on a synchrotron source, have orthorhombic symmetry and belong to space group P2(1)2(1)2. Attempts are being made to solve the structure by MAD and MR.
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Affiliation(s)
- Alex Theodossis
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
| | - Christine C. Milburn
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
| | - Narinder I. Heyer
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Henry J. Lamble
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - David W. Hough
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Michael J. Danson
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Garry L. Taylor
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
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Lamble HJ, Milburn CC, Taylor GL, Hough DW, Danson MJ. Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway in Sulfolobus solfataricus. FEBS Lett 2004; 576:133-6. [PMID: 15474024 DOI: 10.1016/j.febslet.2004.08.074] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [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: 06/28/2004] [Revised: 08/20/2004] [Accepted: 08/23/2004] [Indexed: 11/26/2022]
Abstract
An investigation has been carried out into gluconate dehydratase from the hyperthermophilic Archaeon Sulfolobus solfataricus. The enzyme has been purified from cell extracts of the organism and found to be responsible for both gluconate and galactonate dehydratase activities. It was shown to be a 45 kDa monomer with a half-life of 41 min at 95 degrees C and it exhibited similar catalytic efficiency with both substrates. Taken alongside the recent work on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase, this report clearly demonstrates that the entire non-phosphorylative Entner-Doudoroff pathway of S. solfataricus is promiscuous for the metabolism of both glucose and galactose.
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Affiliation(s)
- Henry J Lamble
- Department of Biology and Biochemistry, Centre for Extremophile Research, University of Bath, Bath BA2 7AY, UK
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44
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Theodossis A, Walden H, Westwick EJ, Connaris H, Lamble HJ, Hough DW, Danson MJ, Taylor GL. The Structural Basis for Substrate Promiscuity in 2-Keto-3-deoxygluconate Aldolase from the Entner-Doudoroff Pathway in Sulfolobus solfataricus. J Biol Chem 2004; 279:43886-92. [PMID: 15265860 DOI: 10.1074/jbc.m407702200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic Archaea Sulfolobus solfataricus grows optimally above 80 degrees C and metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to D-2-keto-3-deoxygluconate (KDG). KDG aldolase (KDGA) then catalyzes the cleavage of KDG to D-glyceraldehyde and pyruvate. It has recently been shown that all the enzymes of this pathway exhibit a catalytic promiscuity that also enables them to be used for the metabolism of galactose. This phenomenon, known as metabolic pathway promiscuity, depends crucially on the ability of KDGA to cleave KDG and D-2-keto-3-deoxygalactonate (KDGal), in both cases producing pyruvate and D-glyceraldehyde. In turn, the aldolase exhibits a remarkable lack of stereoselectivity in the condensation reaction of pyruvate and D-glyceraldehyde, forming a mixture of KDG and KDGal. We now report the structure of KDGA, determined by multiwavelength anomalous diffraction phasing, and confirm that it is a member of the tetrameric N-acetylneuraminate lyase superfamily of Schiff base-forming aldolases. Furthermore, by soaking crystals of the aldolase at more than 80 degrees C below its temperature activity optimum, we have been able to trap Schiff base complexes of the natural substrates pyruvate, KDG, KDGal, and pyruvate plus D-glyceraldehyde, which have allowed rationalization of the structural basis of promiscuous substrate recognition and catalysis. It is proposed that the active site of the enzyme is rigid to keep its thermostability but incorporates extra functionality to be promiscuous.
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Affiliation(s)
- Alex Theodossis
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, Fife KY16 9ST, Scotland
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45
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Walden H, Taylor GL, Lorentzen E, Pohl E, Lilie H, Schramm A, Knura T, Stubbe K, Tjaden B, Hensel R. Structure and Function of a Regulated Archaeal Triosephosphate Isomerase Adapted to High Temperature. J Mol Biol 2004; 342:861-75. [PMID: 15342242 DOI: 10.1016/j.jmb.2004.07.067] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [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: 01/12/2004] [Revised: 06/28/2004] [Accepted: 07/08/2004] [Indexed: 11/19/2022]
Abstract
Triosephophate isomerase (TIM) is a dimeric enzyme in eucarya, bacteria and mesophilic archaea. In hyperthermophilic archaea, however, TIM exists as a tetramer composed of monomers that are about 10% shorter than other eucaryal and bacterial TIM monomers. We report here the crystal structure of TIM from Thermoproteus tenax, a hyperthermophilic archaeon that has an optimum growth temperature of 86 degrees C. The structure was determined from both a hexagonal and an orthorhombic crystal form to resolutions of 2.5A and 2.3A, and refined to R-factors of 19.7% and 21.5%, respectively. In both crystal forms, T.tenax TIM exists as a tetramer of the familiar (betaalpha)(8)-barrel. In solution, however, and unlike other hyperthermophilic TIMs, the T.tenax enzyme exhibits an equilibrium between inactive dimers and active tetramers, which is shifted to the tetramer state through a specific interaction with glycerol-1-phosphate dehydrogenase of T.tenax. This observation is interpreted in physiological terms as a need to reduce the build-up of thermolabile metabolic intermediates that would be susceptible to destruction by heat. A detailed structural comparison with TIMs from organisms with growth optima ranging from 15 degrees C to 100 degrees C emphasizes the importance in hyperthermophilic proteins of the specific location of ionic interactions for thermal stability rather than their numbers, and shows a clear correlation between the reduction of heat-labile, surface-exposed Asn and Gln residues with thermoadaptation. The comparison confirms the increase in charged surface-exposed residues at the expense of polar residues.
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Affiliation(s)
- Helen Walden
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
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46
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Bell GS, Russell RJM, Connaris H, Hough DW, Danson MJ, Taylor GL. Stepwise adaptations of citrate synthase to survival at life's extremes. From psychrophile to hyperthermophile. Eur J Biochem 2002; 269:6250-60. [PMID: 12473121 DOI: 10.1046/j.1432-1033.2002.03344.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The crystal structure of citrate synthase from the thermophilic Archaeon Sulfolobus solfataricus (optimum growth temperature = 85 degrees C) has been determined, extending the number of crystal structures of citrate synthase from different organisms to a total of five that span the temperature range over which life exists (from psychrophile to hyperthermophile). Detailed structural analysis has revealed possible molecular mechanisms that determine the different stabilities of the five proteins. The key to these mechanisms is the precise structural location of the additional interactions. As one ascends the temperature ladder, the subunit interface of this dimeric enzyme and loop regions are reinforced by complex electrostatic interactions, and there is a reduced exposure of hydrophobic surface. These observations reveal a progressive pattern of stabilization through multiple additional interactions at solvent exposed, loop and interfacial regions.
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Affiliation(s)
- Graeme S Bell
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, UK
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Takimoto T, Taylor GL, Connaris HC, Crennell SJ, Portner A. Role of the hemagglutinin-neuraminidase protein in the mechanism of paramyxovirus-cell membrane fusion. J Virol 2002; 76:13028-33. [PMID: 12438628 PMCID: PMC136693 DOI: 10.1128/jvi.76.24.13028-13033.2002] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.7] [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] [Indexed: 11/20/2022] Open
Abstract
Paramyxovirus infects cells by initially attaching to a sialic acid-containing cellular receptor and subsequently fusing with the plasma membrane of the cells. Hemagglutinin-neuraminidase (HN) protein, which is responsible for virus attachment, interacts with the fusion protein in a virus type-specific manner to induce efficient membrane fusion. To elucidate the mechanism of HN-promoted membrane fusion, we characterized a series of Newcastle disease virus HN proteins whose surface residues were mutated. Fusion promotion activity was substantially altered in only the HN proteins with a mutation in the first or sixth beta sheet. These regions overlap the large hydrophobic surface of HN; thus, the hydrophobic surface may contain the fusion promotion domain. Furthermore, a comparison of the HN structure crystallized alone or in complex with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid revealed substantial conformational changes in several loops within or near the hydrophobic surface. Our results suggest that the binding of HN protein to the receptor induces the conformational change of residues near the hydrophobic surface of HN protein and that this change triggers the activation of the F protein, which initiates membrane fusion.
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Affiliation(s)
- Toru Takimoto
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA.
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Gray CC, Smolenski RT, Amrani M, Taylor GL, Yacoub MH. Influence of age and heat stress on cardiac function and nucleotide levels. Adv Exp Med Biol 2002; 486:153-7. [PMID: 11783475 DOI: 10.1007/0-306-46843-3_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- C C Gray
- Department of Cardiothoracic Surgery Heart Science Centre, Imperial College School of Medicine at Harefield Hospital, London, UK
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Wardleworth BN, Russell RJ, White MF, Taylor GL. Preliminary crystallographic studies of the double-stranded DNA-binding protein Sso10b from Sulfolobus solfataricus. Acta Crystallogr D Biol Crystallogr 2001; 57:1893-4. [PMID: 11717508 DOI: 10.1107/s0907444901015517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2001] [Accepted: 09/21/2001] [Indexed: 11/11/2022]
Abstract
Crystals of Sso10b from the hyperthermophilic archaeon Sulfolobus solfataricus have been grown that diffract to 2.6 A resolution. The protein is a highly abundant non-specific double-stranded DNA-binding protein, conserved throughout the archaea, that has been implicated in playing a role in the architecture of archaeal chromatin.
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Affiliation(s)
- B N Wardleworth
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
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Abstract
Comparative structural studies on proteins derived from organisms with growth optima ranging from 15 to 100 degrees C are beginning to shed light on the mechanisms of protein thermoadaptation. One means of sustaining hyperthermostability is for proteins to exist in higher oligomeric forms than their mesophilic homologues. Triosephosphate isomerase (TIM) is one of the most studied enzymes, whose fold represents one of nature's most common protein architectures. Most TIMs are dimers of approximately 250 amino acid residues per monomer. Here, we report the 2.7 A resolution crystal structure of the extremely thermostable TIM from Pyrococcus woesei, a hyperthermophilic archaeon growing optimally at 100 degrees C, representing the first archaeal TIM structure. P. woesei TIM exists as a tetramer comprising monomers of only 228 amino acid residues. Structural comparisons with other less thermostable TIMs show that although the central beta-barrel is largely conserved, severe pruning of several helices and truncation of some loops give rise to a much more compact monomer in the small hyperthermophilic TIM. The classical TIM dimer formation is conserved in P. woesei TIM. The extreme thermostability of PwTIM appears to be achieved by the creation of a compact tetramer where two classical TIM dimers interact via an extensive hydrophobic interface. The tetramer is formed through largely hydrophobic interactions between some of the pruned helical regions. The equivalent helical regions in less thermostable dimeric TIMs represent regions of high average temperature factor. The PwTIM seems to have removed these regions of potential instability in the formation of the tetramer. This study of PwTIM provides further support for the role of higher oligomerisation states in extreme thermal stabilisation.
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Affiliation(s)
- H Walden
- Centre for Biomolecular Sciences, The University of St Andrews, Fife, KY16 9ST, Scotland
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