2j7a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:12, 6 November 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2j7a.png|left|200px]]
 
-
<!--
+
==Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris==
-
The line below this paragraph, containing "STRUCTURE_2j7a", creates the "Structure Box" on the page.
+
<StructureSection load='2j7a' size='340' side='right'caption='[[2j7a]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
{{STRUCTURE_2j7a| PDB=2j7a | SCENE= }}
+
<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]]
 +
Check<jmol>
 +
<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/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2j7a ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===CRYSTAL STRUCTURE OF CYTOCHROME C NITRITE REDUCTASE NRFHA COMPLEX FROM DESULFOVIBRIO VULGARIS===
+
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<ref>PMID:17139260</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2j7a" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_17139260}}, adds the Publication Abstract to the page
+
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 17139260 is the PubMed ID number.
+
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_17139260}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
2J7A is a 18 chains structure of sequences from [http://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].
+
[[Category: Desulfovibrio vulgaris str. Hildenborough]]
-
 
+
[[Category: Large Structures]]
-
==Reference==
+
[[Category: Archer M]]
-
<ref group="xtra">PMID:17139260</ref><references group="xtra"/>
+
[[Category: Oliveira TF]]
-
[[Category: Desulfovibrio vulgaris]]
+
[[Category: Pereira IAC]]
-
[[Category: Archer, M.]]
+
[[Category: Rodrigues ML]]
-
[[Category: Oliveira, T.]]
+
-
[[Category: Pereira, I A.C.]]
+
-
[[Category: Rodrigues, M L.]]
+
-
[[Category: Cytochrome c nitrite reductase]]
+
-
[[Category: Membrane complex]]
+
-
[[Category: Napc/nirt family]]
+
-
[[Category: Nrfa]]
+
-
[[Category: Nrfh]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Quinol dehydrogenase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 01:36:10 2009''
+

Current revision

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

PDB ID 2j7a

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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