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| | <StructureSection load='2vr0' size='340' side='right'caption='[[2vr0]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='2vr0' size='340' side='right'caption='[[2vr0]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vr0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VR0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vr0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VR0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HQO:2-HEPTYL-4-HYDROXY+QUINOLINE+N-OXIDE'>HQO</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]] 2.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j7a|2j7a]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HQO:2-HEPTYL-4-HYDROXY+QUINOLINE+N-OXIDE'>HQO</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </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=2vr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vr0 OCA], [https://pdbe.org/2vr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vr0 RCSB], [https://www.ebi.ac.uk/pdbsum/2vr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vr0 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=2vr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vr0 OCA], [https://pdbe.org/2vr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vr0 RCSB], [https://www.ebi.ac.uk/pdbsum/2vr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vr0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NRFA_DESVH NRFA_DESVH] Catalytic subunit of the cytochrome c nitrite reductase holocomplex NrfHA (PubMed:11004582, PubMed:25534748, PubMed:17139260, PubMed:18597779). Has both nitrite and sulfite reductase activities (PubMed:11004582). Catalyzes the reduction of nitrite to ammonia, consuming six electrons acquired by the electron donor subunit NrfH from the menaquinone pool, in an anaerobic respiratory process of nitrite (PubMed:11004582, PubMed:25534748, PubMed:17139260, PubMed:18597779). The other biological function of the NrfHA holocomplex is to detoxify nitrite (PubMed:15547266, PubMed:25534748). This function is essential for the survival of this organism as it enables it to overcome inhibition by nitrite, which is produced by other organisms living in the same environment (Probable).<ref>PMID:11004582</ref> <ref>PMID:15547266</ref> <ref>PMID:17139260</ref> <ref>PMID:18597779</ref> <ref>PMID:25534748</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| - | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Desulfovibrio vulgaris]] | + | [[Category: Desulfovibrio vulgaris str. Hildenborough]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Archer, M]] | + | [[Category: Archer M]] |
| - | [[Category: Rodrigues, M L]] | + | [[Category: Rodrigues ML]] |
| - | [[Category: Hqno]]
| + | |
| - | [[Category: Membrane complex]]
| + | |
| - | [[Category: Nrfh]]
| + | |
| - | [[Category: Nrfha]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Quinol dehydrogenase]]
| + | |
| Structural highlights
Function
NRFA_DESVH Catalytic subunit of the cytochrome c nitrite reductase holocomplex NrfHA (PubMed:11004582, PubMed:25534748, PubMed:17139260, PubMed:18597779). Has both nitrite and sulfite reductase activities (PubMed:11004582). Catalyzes the reduction of nitrite to ammonia, consuming six electrons acquired by the electron donor subunit NrfH from the menaquinone pool, in an anaerobic respiratory process of nitrite (PubMed:11004582, PubMed:25534748, PubMed:17139260, PubMed:18597779). The other biological function of the NrfHA holocomplex is to detoxify nitrite (PubMed:15547266, PubMed:25534748). This function is essential for the survival of this organism as it enables it to overcome inhibition by nitrite, which is produced by other organisms living in the same environment (Probable).[1] [2] [3] [4] [5]
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
Membrane-bound cytochrome c quinol dehydrogenases play a crucial role in bacterial respiration by oxidizing menaquinol and transferring electrons to various periplasmic oxidoreductases. In this work, the menaquinol oxidation site of NrfH was characterized by the determination of the X-ray structure of Desulfovibrio vulgaris NrfHA nitrite reductase complex bound to 2-heptyl-4-hydroxyquinoline-N-oxide, which is shown to act as a competitive inhibitor of NrfH quinol oxidation activity. The structure, at 2.8-A resolution, reveals that the inhibitor binds close to NrfH heme 1, where it establishes polar contacts with two essential residues: Asp89, the residue occupying the heme distal ligand position, and Lys82, a strictly conserved residue. The menaquinol binding cavity is largely polar and has a wide opening to the protein surface. Coarse-grained molecular dynamics simulations suggest that the quinol binding site of NrfH and several other respiratory enzymes lie in the head group region of the membrane, which probably facilitates proton transfer to the periplasm. Although NrfH is not a multi-span membrane protein, its quinol binding site has several characteristics similar to those of quinone binding sites previously described. The data presented here provide the first characterization of the quinol binding site of the cytochrome c quinol dehydrogenase family.
Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA.,Rodrigues ML, Scott KA, Sansom MS, Pereira IA, Archer M J Mol Biol. 2008 Aug 29;381(2):341-50. Epub 2008 Jun 3. PMID:18597779[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pereira IA, LeGall J, Xavier AV, Teixeira M. Characterization of a heme c nitrite reductase from a non-ammonifying microorganism, Desulfovibrio vulgaris Hildenborough. Biochim Biophys Acta. 2000 Aug 31;1481(1):119-30. PMID:11004582 doi:10.1016/s0167-4838(00)00111-4
- ↑ Haveman SA, Greene EA, Stilwell CP, Voordouw JK, Voordouw G. Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris hildenborough by nitrite. J Bacteriol. 2004 Dec;186(23):7944-50. PMID:15547266 doi:10.1128/JB.186.23.7944-7950.2004
- ↑ Rodrigues ML, Oliveira TF, Pereira IA, Archer M. X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination. EMBO J. 2006 Dec 13;25(24):5951-60. Epub 2006 Nov 30. PMID:17139260
- ↑ Rodrigues ML, Scott KA, Sansom MS, Pereira IA, Archer M. Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA. J Mol Biol. 2008 Aug 29;381(2):341-50. Epub 2008 Jun 3. PMID:18597779 doi:10.1016/j.jmb.2008.05.066
- ↑ Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environ Sci Technol. 2015 Jan 20;49(2):924-31. PMID:25534748 doi:10.1021/es504484m
- ↑ Rodrigues ML, Scott KA, Sansom MS, Pereira IA, Archer M. Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA. J Mol Biol. 2008 Aug 29;381(2):341-50. Epub 2008 Jun 3. PMID:18597779 doi:10.1016/j.jmb.2008.05.066
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