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Erdyneeva EB, Radnagurueva AA, Dunaevsky YE, Belkova NL, Namsaraev ZB, Lavrentieva EV. Aminopeptidase Activity of Haloalkalophilic Bacteria of the Genus Halomonas Isolated from the Soda-Saline Lakes in the Badain Jaran Desert. Microbiology (Reading) 2018; 87:538-548. [DOI: 10.1134/s0026261718040069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 07/26/2024] Open
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Characterization of thermostable deblocking aminopeptidases of archaeon Thermococcus onnurineus NA1 by proteomic and biochemical approaches. J Microbiol 2012; 50:792-7. [PMID: 23124747 DOI: 10.1007/s12275-012-2461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022]
Abstract
Thermococcus onnurineus NA1 is a hyperthermophilic archaeon that grows optimally at >80°C. The deblocking aminopeptidase (DAP) (TNA1-DAP1) encoded in Ton_1032 of T. onnurineus NA1 is considered a major DAP. However, four genes encoding putative DAP have been identified from a genomic analysis of T. onnurineus NA1. A proteomic analysis revealed that all four DAPs were differentially induced in YPS culture medium and, particularly, two DAPs (TNA1-DAP1 and TNA1-DAP2) were dominantly expressed in T. onnurineus NA1. The biochemical properties and enzyme activity of DAPs induced in an E. coli expression system suggested that the two major DAPs play complementary roles in T. onnurineus NA1.
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Talon R, Kahn R, Durá MA, Maury O, Vellieux FMD, Franzetti B, Girard E. Using lanthanoid complexes to phase large macromolecular assemblies. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:74-8. [PMID: 21169697 PMCID: PMC3004260 DOI: 10.1107/s0909049510036824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 09/14/2010] [Indexed: 05/08/2023]
Abstract
Lanthanoid ions exhibit extremely large anomalous X-ray scattering at their L(III) absorption edge. They are thus well suited for anomalous diffraction experiments. A novel class of lanthanoid complexes has been developed that combines the physical properties of lanthanoid atoms with functional chemical groups that allow non-covalent binding to proteins. Two structures of large multimeric proteins have already been determined by using such complexes. Here the use of the luminescent europium tris-dipicolinate complex [Eu(DPA)(3)](3-) to solve the low-resolution structure of a 444 kDa homododecameric aminopeptidase, called PhTET1-12s from the archaea Pyrococcus horikoshii, is reported. Surprisingly, considering the low resolution of the data, the experimental electron density map is very well defined. Experimental phases obtained by using the lanthanoid complex lead to maps displaying particular structural features usually observed in higher-resolution maps. Such complexes open a new way for solving the structure of large molecular assemblies, even with low-resolution data.
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Affiliation(s)
- Romain Talon
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Richard Kahn
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - M. Asunción Durá
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Olivier Maury
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Chimie, UMR CNRS 5182, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Frédéric M. D. Vellieux
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Bruno Franzetti
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Eric Girard
- CEA, IBS, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
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Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A. The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta. PLoS Biol 2009; 7:e43. [PMID: 19243223 PMCID: PMC2652392 DOI: 10.1371/journal.pbio.1000043] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 01/12/2009] [Indexed: 01/07/2023] Open
Abstract
Heme is a ligand for the human nuclear receptors (NR) REV-ERBalpha and REV-ERBbeta, which are transcriptional repressors that play important roles in circadian rhythm, lipid and glucose metabolism, and diseases such as diabetes, atherosclerosis, inflammation, and cancer. Here we show that transcription repression mediated by heme-bound REV-ERBs is reversed by the addition of nitric oxide (NO), and that the heme and NO effects are mediated by the C-terminal ligand-binding domain (LBD). A 1.9 A crystal structure of the REV-ERBbeta LBD, in complex with the oxidized Fe(III) form of heme, shows that heme binds in a prototypical NR ligand-binding pocket, where the heme iron is coordinately bound by histidine 568 and cysteine 384. Under reducing conditions, spectroscopic studies of the heme-REV-ERBbeta complex reveal that the Fe(II) form of the LBD transitions between penta-coordinated and hexa-coordinated structural states, neither of which possess the Cys384 bond observed in the oxidized state. In addition, the Fe(II) LBD is also able to bind either NO or CO, revealing a total of at least six structural states of the protein. The binding of known co-repressors is shown to be highly dependent upon these various liganded states. REV-ERBs are thus highly dynamic receptors that are responsive not only to heme, but also to redox and gas. Taken together, these findings suggest new mechanisms for the systemic coordination of molecular clocks and metabolism. They also raise the possibility for gas-based therapies for the many disorders associated with REV-ERB biological functions.
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Affiliation(s)
- Keith I Pardee
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | - Xiaohui Xu
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
- Midwest Center for Structural Genomics, University of Toronto, Toronto, Canada
| | - Jeff Reinking
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Biology, State University of New York at New Paltz, New Paltz, New York, United States of America
| | - Anja Schuetz
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Suya Liu
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Rongguang Zhang
- Midwest Center for Structural Genomics, Argonne National Lab, Argonne, Illinois, United States of America
| | - Jens Tiefenbach
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | - Gilles Lajoie
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | | | - Alexey Botchkarev
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Henry M Krause
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
- * To whom correspondence should be addressed. E-mail: (AE); (HMK)
| | - Aled Edwards
- Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
- Midwest Center for Structural Genomics, University of Toronto, Toronto, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
- * To whom correspondence should be addressed. E-mail: (AE); (HMK)
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Lee HS, Cho Y, Kim YJ, Nam K, Lee JH, Kang SG. Biochemical characterization of deblocking aminopeptidase from hyperthermophilic archaeon Thermococcus onnurineus NA1. J Biosci Bioeng 2007; 104:188-94. [PMID: 17964482 DOI: 10.1263/jbb.104.188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 06/11/2007] [Indexed: 11/17/2022]
Abstract
A genomic analysis of the hyperthermophilic archaeon Thermoccoccus onnurineus NA1 (TNA1) revealed the presence of a deblocking aminopeptidase (DAP) gene with high similarity to the genes of DAPs from Pyrococcus furiosus (86%) and Pyrococcus horikoshii (83% identity). The optimum aminopeptidase activity of the recombinant enzyme was observed at pH 7.5 and in the range of 90 degrees C to 100 degrees C. The specific aminopeptidase and deblocking activities of the enzyme toward Leu-pNA and Ac-Leu-pNA were 18- and 3-fold higher than those of a P. horikoshii DAP (DAP2), respectively. The enzyme activity was significantly increased by Co(2+) ions. The presence of Co(2+) ions induced the activation of the enzyme with heating and changed the large oligomer to a dimer. The enzyme activated by Co(2+) ions appeared to eventually be inactivated by autodegradation, which was confirmed by mass spectrometry.
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Affiliation(s)
- Hyun Sook Lee
- Korea Ocean Research & Development Institute, Ansan P.O. Box 29, Seoul 425-600, Korea
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Schoehn G, Vellieux FMD, Asunción Durá M, Receveur-Bréchot V, Fabry CMS, Ruigrok RWH, Ebel C, Roussel A, Franzetti B. An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron. J Biol Chem 2006; 281:36327-37. [PMID: 16973604 DOI: 10.1074/jbc.m604417200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.
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Affiliation(s)
- Guy Schoehn
- Laboratoire de Virologie Moléculaire et Structurale c/o EMBL, FRE 2854 CNRS-UJF, 38042 Grenoble, France
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