2j7a

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

Structural highlights

2j7a is a 18 chain structure with sequence from Desulfovibrio vulgaris str. Hildenborough. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[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

Oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate ATP by oxidative phosphorylation. A novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. Here, we describe the first structure of a cytochrome from this family, NrfH from Desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome c nitrite reductase NrfA. One NrfH molecule interacts with one NrfA dimer in an asymmetrical manner, forming a large membrane-bound complex with an overall alpha(4)beta(2) quaternary arrangement. The menaquinol-interacting NrfH haem is pentacoordinated, bound by a methionine from the CXXCHXM sequence, with an aspartate residue occupying the distal position. The NrfH haem that transfers electrons to NrfA has a lysine residue from the closest NrfA molecule as distal ligand. A likely menaquinol binding site, containing several conserved and essential residues, is identified.

X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.,Rodrigues ML, Oliveira TF, Pereira IA, Archer M EMBO J. 2006 Dec 13;25(24):5951-60. Epub 2006 Nov 30. PMID:17139260^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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, 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2j7a"

@@ Line 3: / Line 3: @@
 <StructureSection load='2j7a' size='340' side='right'caption='[[2j7a]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2j7a]] is a 18 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=2J7A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2j7a]] is a 18 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=2J7A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</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]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</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=2j7a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7a OCA], [https://pdbe.org/2j7a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7a RCSB], [https://www.ebi.ac.uk/pdbsum/2j7a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7a ProSAT]</span></td></tr>
 </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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 12: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/2j7a_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>
   </jmolCheckbox>
@@ Line 30: / Line 33: @@
 *[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
 *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
-*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio vulgaris]]
+[[Category: Desulfovibrio vulgaris str. Hildenborough]]
 [[Category: Large Structures]]
-[[Category: Archer, M]]
+[[Category: Archer M]]
-[[Category: Oliveira, T F]]
+[[Category: Oliveira TF]]
-[[Category: Pereira, I A.C]]
+[[Category: Pereira IAC]]
-[[Category: Rodrigues, M L]]
+[[Category: Rodrigues ML]]
-[[Category: Cytochrome c nitrite reductase]]
-[[Category: Membrane complex]]
-[[Category: Napc/nirt family]]
-[[Category: Nrfa]]
-[[Category: Nrfh]]
-[[Category: Oxidoreductase]]
-[[Category: Quinol dehydrogenase]]

2j7a

From Proteopedia

Current revision

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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