|
|
| (2 intermediate revisions not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='1wui' size='340' side='right'caption='[[1wui]], [[Resolution|resolution]] 1.04Å' scene=''> | | <StructureSection load='1wui' size='340' side='right'caption='[[1wui]], [[Resolution|resolution]] 1.04Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wui]] is a 2 chain structure with sequence from [http://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=1WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wui]] 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=1WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUI 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=NFC:NI-FE+ACTIVE+CENTER+A-FORM'>NFC</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]] 1.04Å</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=NFC:NI-FE+ACTIVE+CENTER+A-FORM'>NFC</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wuh|1wuh]], [[1wuj|1wuj]], [[1wuk|1wuk]], [[1wul|1wul]]</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=1wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wui OCA], [https://pdbe.org/1wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wui RCSB], [https://www.ebi.ac.uk/pdbsum/1wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wui ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wui OCA], [http://pdbe.org/1wui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wui RCSB], [http://www.ebi.ac.uk/pdbsum/1wui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wui 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. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 17: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wu/1wui_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wu/1wui_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cytochrome-c3 hydrogenase]]
| + | [[Category: Desulfovibrio vulgaris str. 'Miyazaki F']] |
| - | [[Category: Desulfovibrio vulgaris str. 'miyazaki f']] | + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Higuchi, Y]] | + | [[Category: Higuchi Y]] |
| - | [[Category: Hirota, S]] | + | [[Category: Hirota S]] |
| - | [[Category: Kano, K]] | + | [[Category: Kano K]] |
| - | [[Category: Kato, T]] | + | [[Category: Kato T]] |
| - | [[Category: Komori, H]] | + | [[Category: Komori H]] |
| - | [[Category: Nakahara, A]] | + | [[Category: Nakahara A]] |
| - | [[Category: Ogata, H]] | + | [[Category: Ogata H]] |
| - | [[Category: Shibata, N]] | + | [[Category: Shibata N]] |
| - | [[Category: High resolution crystal structure]]
| + | |
| - | [[Category: Ni-a state]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Unready state]]
| + | |
| Structural highlights
1wui 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 1.04Å |
| 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.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices.
Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state.,Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y Structure. 2005 Nov;13(11):1635-42. PMID:16271886[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y. Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state. Structure. 2005 Nov;13(11):1635-42. PMID:16271886 doi:10.1016/j.str.2005.07.018
|
