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| | <StructureSection load='1dvb' size='340' side='right'caption='[[1dvb]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='1dvb' size='340' side='right'caption='[[1dvb]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1dvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_subsp._vulgaris_str._hildenborough Desulfovibrio vulgaris subsp. vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DVB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1dvb]] is a 1 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=1DVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.9Å</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=1dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvb OCA], [http://pdbe.org/1dvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dvb RCSB], [http://www.ebi.ac.uk/pdbsum/1dvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvb ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvb OCA], [https://pdbe.org/1dvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvb RCSB], [https://www.ebi.ac.uk/pdbsum/1dvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity). | + | [https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Desulfovibrio vulgaris subsp. vulgaris str. hildenborough]] | + | [[Category: Desulfovibrio vulgaris str. Hildenborough]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Holmes, M]] | + | [[Category: Holmes M]] |
| - | [[Category: Legall, J]] | + | [[Category: Le Trong I]] |
| - | [[Category: Liu, M Y]] | + | [[Category: Legall J]] |
| - | [[Category: Sieker, L C]] | + | [[Category: Liu MY]] |
| - | [[Category: Stenkamp, R E]] | + | [[Category: Sieker LC]] |
| - | [[Category: Trong, I Le]] | + | [[Category: Stenkamp RE]] |
| - | [[Category: Turley, S]] | + | [[Category: Turley S]] |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Ferroxidase]]
| + | |
| - | [[Category: Iron]]
| + | |
| Structural highlights
Function
RUBY_DESVH May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
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
Rubrerythrin is a non-heme iron dimeric protein isolated from the sulfate-reducing bacterium Desulfovibrio vulgaris. Each monomer has one mononuclear iron center similar to rubredoxin and one dinuclear metal center similar to hemerythrin or ribonucleotide reductase. The 1.88 A X-ray structure of the "as isolated" molecule and a uranyl heavy atom derivative have been solved by molecular replacement techniques. The resulting model of the native "as isolated" molecule, including 164 water molecules, has been refined giving a final R factor of 0.197 (R(free) = 0.255). The structure has the same general protein fold, domain structure, and dimeric interactions as previously found for rubrerythrin [1, 2], but it also has some interesting undetected differences at the metal centers. The refined model of the protein structure has a cis peptide between residues 78 and 79. The Fe-Cys4 center has a previously undetected strong seventh N-H...S hydrogen bond in addition to the six N-H...S bonds usually found in rubredoxin. The dinuclear metal center has a hexacoordinate Fe atom and a tetracoordinate Zn atom. Each metal is coordinated by a GluXXHis polypeptide chain segment. The Zn atom binds at a site distinctly different from that found in the structure of a diiron rubrerythrin. Difference electron density for the uranyl derivative shows an extremely large peak adjacent to and replacing the Zn atom, indicating that this particular site is capable of binding other atoms. This feature/ability may give rise to some of the confusing activities ascribed to this molecule.
The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results.,Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:10968622[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE. The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results. J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:10968622
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