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| | <StructureSection load='3cus' size='340' side='right'caption='[[3cus]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='3cus' size='340' side='right'caption='[[3cus]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3cus]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_49200 Atcc 49200]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CUS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3cus]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Solidesulfovibrio_fructosivorans Solidesulfovibrio fructosivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CUS 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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.2Å</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=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1frf|1frf]], [[1yrq|1yrq]], [[1yqw|1yqw]], [[3cur|3cur]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hydA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=878 ATCC 49200]), hydB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=878 ATCC 49200])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c3_hydrogenase Cytochrome-c3 hydrogenase], with EC number [https://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=3cus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cus OCA], [https://pdbe.org/3cus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cus RCSB], [https://www.ebi.ac.uk/pdbsum/3cus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cus 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=3cus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cus OCA], [https://pdbe.org/3cus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cus RCSB], [https://www.ebi.ac.uk/pdbsum/3cus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cus ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PHNS_DESFR PHNS_DESFR]] Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.
| + | [https://www.uniprot.org/uniprot/PHNS_SOLFR PHNS_SOLFR] Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 49200]] | |
| - | [[Category: Cytochrome-c3 hydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Volbeda, A]] | + | [[Category: Solidesulfovibrio fructosivorans]] |
| - | [[Category: Iron]] | + | [[Category: Volbeda A]] |
| - | [[Category: Iron-sulfur]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Ni-fe hydrogenase tunnel mutant]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
3cus is a 6 chain structure with sequence from Solidesulfovibrio fructosivorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PHNS_SOLFR Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.
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, which catalyze H(2) to H(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H(2) toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these.
Experimental approaches to kinetics of gas diffusion in hydrogenase.,Leroux F, Dementin S, Burlat B, Cournac L, Volbeda A, Champ S, Martin L, Guigliarelli B, Bertrand P, Fontecilla-Camps J, Rousset M, Leger C Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11188-93. Epub 2008 Aug 6. PMID:18685111[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Leroux F, Dementin S, Burlat B, Cournac L, Volbeda A, Champ S, Martin L, Guigliarelli B, Bertrand P, Fontecilla-Camps J, Rousset M, Leger C. Experimental approaches to kinetics of gas diffusion in hydrogenase. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11188-93. Epub 2008 Aug 6. PMID:18685111
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