1h2a

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[[Image:1h2a.jpg|left|200px]]
 
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==SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS==
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The line below this paragraph, containing "STRUCTURE_1h2a", creates the "Structure Box" on the page.
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<StructureSection load='1h2a' size='340' side='right'caption='[[1h2a]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1h2a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._'Miyazaki_F' Desulfovibrio vulgaris str. 'Miyazaki F']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H2A FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFE:NI-FE+ACTIVE+CENTER'>NFE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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{{STRUCTURE_1h2a| PDB=1h2a | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h2a OCA], [https://pdbe.org/1h2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h2a RCSB], [https://www.ebi.ac.uk/pdbsum/1h2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h2a ProSAT]</span></td></tr>
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</table>
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'''SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS'''
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== Function ==
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[https://www.uniprot.org/uniprot/PHNS_DESVM PHNS_DESVM] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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BACKGROUND: The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase. RESULTS: The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center. CONCLUSIONS: From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h2/1h2a_consurf.spt"</scriptWhenChecked>
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1H2A is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2A OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis., Higuchi Y, Yagi T, Yasuoka N, Structure. 1997 Dec 15;5(12):1671-80. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9438867 9438867]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h2a ConSurf].
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[[Category: Desulfovibrio vulgaris]]
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<div style="clear:both"></div>
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[[Category: Ferredoxin hydrogenase]]
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__TOC__
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[[Category: Protein complex]]
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</StructureSection>
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[[Category: Higuchi, Y.]]
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[[Category: Desulfovibrio vulgaris str. 'Miyazaki F']]
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[[Category: Yasuoka, N.]]
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[[Category: Large Structures]]
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[[Category: Hydrogen metabolism]]
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[[Category: Higuchi Y]]
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[[Category: Mad]]
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[[Category: Yasuoka N]]
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[[Category: Mg center]]
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[[Category: Mir]]
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[[Category: Ni-fe hydrogenase]]
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[[Category: Oxidoreductase]]
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[[Category: So ligand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 18:19:52 2008''
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Current revision

SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS

PDB ID 1h2a

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