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| | <StructureSection load='5y4n' size='340' side='right'caption='[[5y4n]], [[Resolution|resolution]] 1.69Å' scene=''> | | <StructureSection load='5y4n' size='340' side='right'caption='[[5y4n]], [[Resolution|resolution]] 1.69Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvm Desvm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y4N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y4n]] 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=5Y4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y4N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.69Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c3_hydrogenase Cytochrome-c3 hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.2.1 1.12.2.1] </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=5y4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y4n OCA], [https://pdbe.org/5y4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y4n RCSB], [https://www.ebi.ac.uk/pdbsum/5y4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y4n ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y4n OCA], [http://pdbe.org/5y4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y4n RCSB], [http://www.ebi.ac.uk/pdbsum/5y4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y4n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PHNS_DESVM PHNS_DESVM]] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. [[http://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_NITV9 PHNS_NITV9] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cytochrome-c3 hydrogenase]] | + | [[Category: Desulfovibrio vulgaris str. 'Miyazaki F']] |
| - | [[Category: Desvm]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Higuchi, Y]] | + | [[Category: Higuchi Y]] |
| - | [[Category: Hiromoto, T]] | + | [[Category: Hiromoto T]] |
| - | [[Category: Mochida, S]] | + | [[Category: Mochida S]] |
| - | [[Category: Nishikawa, K]] | + | [[Category: Nishikawa K]] |
| - | [[Category: Shibata, N]] | + | [[Category: Shibata N]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
5y4n is a 2 chain structure with sequence from Desulfovibrio vulgaris str. 'Miyazaki F'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.69Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PHNS_NITV9 Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.
Publication Abstract from PubMed
Hydrogenase is a key enzyme for a coming hydrogen energy society, because it has strong catalytic activities on both uptake and production of dihydrogen. We, however, have to overcome the sensitivity against O2 of the enzyme, because hydrogenase is, generally, easily inactivated in the presence of O2. In this study, we have revisited the crystal structures of [NiFe]hydrogenase from sulfate-reducing bacterium in the several oxidized and reduced conditions. Our results revealed that the Ni-Fe active site of the enzyme exposed into O2 showed two forms, Form-1 and Form-2. The Ni-Fe active site in Form-1 showed the typical Ni-B (inactive ready) structure, whereas those in Form-2 lost Ni with no relation to an exposure time to O2, and two cysteinyl sulfur ligands made a disulfide bond. On the other hand, the formation of sulfenylation of the cysteinyl ligand to Ni, which is often observed in the oxidized form, did not correlate with the Ni-elimination, but with exposure time to O2.
Ni-elimination from the active site of the standard [NiFe]hydrogenase upon oxidation by O2.,Nishikawa K, Mochida S, Hiromoto T, Shibata N, Higuchi Y J Inorg Biochem. 2017 Dec;177:435-437. doi: 10.1016/j.jinorgbio.2017.09.011. Epub, 2017 Sep 14. PMID:28967475[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nishikawa K, Mochida S, Hiromoto T, Shibata N, Higuchi Y. Ni-elimination from the active site of the standard [NiFe]hydrogenase upon oxidation by O2. J Inorg Biochem. 2017 Dec;177:435-437. doi: 10.1016/j.jinorgbio.2017.09.011. Epub, 2017 Sep 14. PMID:28967475 doi:http://dx.doi.org/10.1016/j.jinorgbio.2017.09.011
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