View source for 3ayz


==Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an air-oxidized condition==
<StructureSection load='3ayz' size='340' side='right'caption='[[3ayz]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ayz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hydrogenovibrio_marinus Hydrogenovibrio marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AYZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</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=3ayz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ayz OCA], [https://pdbe.org/3ayz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ayz RCSB], [https://www.ebi.ac.uk/pdbsum/3ayz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ayz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/F2Z6J6_HYDMR F2Z6J6_HYDMR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2) --&gt; 2H(+) + 2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32 A. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.

Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.,Shomura Y, Yoon KS, Nishihara H, Higuchi Y Nature. 2011 Oct 16;479(7372):253-6. doi: 10.1038/nature10504. PMID:22002607<ref>PMID:22002607</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ayz" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Hydrogenovibrio marinus]]
[[Category: Large Structures]]
[[Category: Higuchi Y]]
[[Category: Nishihara H]]
[[Category: Shomura Y]]
[[Category: Yoon KS]]