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2kkd

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Revision as of 11:17, 18 July 2018

NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin

Structural highlights

2kkd is a 1 chain structure with sequence from Desvh. This structure supersedes the now removed PDB entry 2qkz. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	8rxn, 2ql0
Gene:	rub, DVU_3184 (DESVH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RUBR_DESVH] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.

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

The Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The betaCH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine Hbeta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.

An NMR structural study of nickel-substituted rubredoxin.,Goodfellow BJ, Duarte IC, Macedo AL, Volkman BF, Nunes SG, Moura I, Markley JL, Moura JJ J Biol Inorg Chem. 2009 Dec 8. PMID:19997764^[1]

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

References

↑ Goodfellow BJ, Duarte IC, Macedo AL, Volkman BF, Nunes SG, Moura I, Markley JL, Moura JJ. An NMR structural study of nickel-substituted rubredoxin. J Biol Inorg Chem. 2009 Dec 8. PMID:19997764 doi:10.1007/s00775-009-0613-6

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==
 <StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[8rxn|8rxn]], [[2ql0|2ql0]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://pdbe.org/2kkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://pdbe.org/2kkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/2kkd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/2kkd_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 41: / Line 42: @@
 [[Category: Nunes, S G]]
 [[Category: Volkman, B F]]
+[[Category: Cytoplasm]]
 [[Category: Electron transport]]
 [[Category: Iron]]
 [[Category: Metal-binding]]
 [[Category: Transport]]

2kkd

From Proteopedia

Revision as of 11:17, 18 July 2018

NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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