1h2a: Difference between revisions

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<StructureSection load='1h2a' size='340' side='right'caption='[[1h2a]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1h2a' size='340' side='right'caption='[[1h2a]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><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>
</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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>
<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>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[[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. [[https://www.uniprot.org/uniprot/PHNL_DESVM PHNL_DESVM]] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.  
[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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:9438867<ref>PMID:9438867</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1h2a" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Desulfovibrio vulgaris str. 'miyazaki f']]
[[Category: Desulfovibrio vulgaris str. 'Miyazaki F']]
[[Category: Ferredoxin hydrogenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Higuchi, Y]]
[[Category: Higuchi Y]]
[[Category: Yasuoka, N]]
[[Category: Yasuoka N]]
[[Category: Hydrogen metabolism]]
[[Category: Mad]]
[[Category: Mg center]]
[[Category: Mir]]
[[Category: Ni-fe hydrogenase]]
[[Category: Oxidoreductase]]
[[Category: So ligand]]
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