2vr0: Difference between revisions
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==Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor== | ==Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor== | ||
<StructureSection load='2vr0' size='340' side='right' | <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 [ | <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=' | </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=' | <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='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'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/NRFA_NITV2 NRFA_NITV2] Catalytic subunit of the cytochrome c nitrite reductase holocomplex NrfHA (PubMed:11004582, PubMed:17139260, PubMed:18597779, PubMed:25534748). 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:17139260, PubMed:18597779, PubMed:25534748). 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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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vr/2vr0_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vr/2vr0_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <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> | ||
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==See Also== | ==See Also== | ||
*[[ | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Desulfovibrio vulgaris]] | [[Category: Desulfovibrio vulgaris str. Hildenborough]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Archer M]] | ||
[[Category: | [[Category: Rodrigues ML]] | ||
Latest revision as of 12:32, 6 November 2024
Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitorCrystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor
Structural highlights
FunctionNRFA_NITV2 Catalytic subunit of the cytochrome c nitrite reductase holocomplex NrfHA (PubMed:11004582, PubMed:17139260, PubMed:18597779, PubMed:25534748). 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:17139260, PubMed:18597779, PubMed:25534748). 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 PubMedMembrane-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 AlsoReferences
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