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| | ==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin== | | ==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=''> | + | <StructureSection load='2kkd' size='340' side='right'caption='[[2kkd]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KKD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[8rxn|8rxn]], [[2ql0|2ql0]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [https://pdbe.org/2kkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [https://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd ProSAT]</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> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RUBR_DESVH 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. | + | [https://www.uniprot.org/uniprot/RUBR_DESVH 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 2kkd" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 2kkd" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Rubredoxin 3D structures|Rubredoxin 3D structures]] |
| | + | *[[Rubredoxin PDB structures|Rubredoxin PDB structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Desvh]] | + | [[Category: Desulfovibrio vulgaris str. Hildenborough]] |
| - | [[Category: Duarte, I C]] | + | [[Category: Large Structures]] |
| - | [[Category: Macedo, A L]] | + | [[Category: Duarte IC]] |
| - | [[Category: Markley, J L]] | + | [[Category: Macedo AL]] |
| - | [[Category: Moura, I]] | + | [[Category: Markley JL]] |
| - | [[Category: Moura, J J.G]] | + | [[Category: Moura I]] |
| - | [[Category: Nunes, S G]] | + | [[Category: Moura JJG]] |
| - | [[Category: Volkman, B F]] | + | [[Category: Nunes SG]] |
| - | [[Category: Cytoplasm]]
| + | [[Category: Volkman BF]] |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Transport]]
| + | |
| Structural highlights
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.
See Also
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
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