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| | ==X-ray structure of E.coli Wrba in complex with FMN at 1.2 A resolution== | | ==X-ray structure of E.coli Wrba in complex with FMN at 1.2 A resolution== |
| - | <StructureSection load='3zho' size='340' side='right' caption='[[3zho]], [[Resolution|resolution]] 1.20Å' scene=''> | + | <StructureSection load='3zho' size='340' side='right'caption='[[3zho]], [[Resolution|resolution]] 1.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3zho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3zho]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 1.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SME:METHIONINE+SULFOXIDE'>SME</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SME:METHIONINE+SULFOXIDE'>SME</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)H_dehydrogenase_(quinone) NAD(P)H dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.2 1.6.5.2] </span></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=3zho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zho OCA], [https://pdbe.org/3zho PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zho RCSB], [https://www.ebi.ac.uk/pdbsum/3zho PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zho 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=3zho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zho OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zho RCSB], [http://www.ebi.ac.uk/pdbsum/3zho PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NQOR_ECOLI NQOR_ECOLI] It seems to function in response to environmental stress when various electron transfer chains are affected or when the environment is highly oxidizing. It reduces quinones to the hydroquinone state to prevent interaction of the semiquinone with O2 and production of superoxide. It prefers NADH over NADPH.<ref>PMID:16672604</ref> <ref>PMID:9694845</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3zho" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Brynda, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Carey, J]] | + | [[Category: Brynda J]] |
| - | [[Category: Ettrich, R]] | + | [[Category: Carey J]] |
| - | [[Category: Kishko, I]] | + | [[Category: Ettrich R]] |
| - | [[Category: Kuty, M]] | + | [[Category: Kishko I]] |
| - | [[Category: Lapkouski, M]] | + | [[Category: Kuty M]] |
| - | [[Category: Smatanova, I K]] | + | [[Category: Lapkouski M]] |
| - | [[Category: Electron transport]]
| + | [[Category: Smatanova IK]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Trp repressor]]
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| Structural highlights
Function
NQOR_ECOLI It seems to function in response to environmental stress when various electron transfer chains are affected or when the environment is highly oxidizing. It reduces quinones to the hydroquinone state to prevent interaction of the semiquinone with O2 and production of superoxide. It prefers NADH over NADPH.[1] [2]
Publication Abstract from PubMed
The Escherichia coli protein WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase, was crystallized under new conditions in the presence of FAD or the native cofactor FMN. Slow-growing deep yellow crystals formed with FAD display the tetragonal bipyramidal shape typical for WrbA and diffract to 1.2 A resolution, the highest yet reported. Faster-growing deep yellow crystals formed with FMN display an atypical shape, but diffract to only approximately 1.6 A resolution and are not analysed further here. The 1.2 A resolution structure detailed here revealed only FMN in the active site and no electron density that can accommodate the missing parts of FAD. The very high resolution supports the modelling of the FMN isoalloxazine with a small but distinct propeller twist, apparently the first experimental observation of this predicted conformation, which appears to be enforced by the protein through a network of hydrogen bonds. Comparison of the electron density of the twisted isoalloxazine ring with the results of QM/MM simulations is compatible with the oxidized redox state. The very high resolution also supports the unique refinement of Met10 as the sulfoxide, confirmed by mass spectrometry. Bond lengths, intramolecular distances, and the pattern of hydrogen-bond donors and acceptors suggest the cofactor may interact with Met10. Slow incorporation of FMN, which is present as a trace contaminant in stocks of FAD, into growing crystals may be responsible for the near-atomic resolution, but a direct effect of the conformation of FMN and/or Met10 sulfoxide cannot be ruled out.
1.2 A resolution crystal structure of Escherichia coli WrbA holoprotein.,Kishko I, Carey J, Reha D, Brynda J, Winkler R, Harish B, Guerra R, Ettrichova O, Kukacka Z, Sheryemyetyeva O, Novak P, Kuty M, Kuta Smatanova I, Ettrich R, Lapkouski M Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1748-57. doi:, 10.1107/S0907444913017162. Epub 2013 Aug 15. PMID:23999298[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Patridge EV, Ferry JG. WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase. J Bacteriol. 2006 May;188(10):3498-506. PMID:16672604 doi:http://dx.doi.org/10.1128/JB.188.10.3498-3506.2006
- ↑ Grandori R, Khalifah P, Boice JA, Fairman R, Giovanielli K, Carey J. Biochemical characterization of WrbA, founding member of a new family of multimeric flavodoxin-like proteins. J Biol Chem. 1998 Aug 14;273(33):20960-6. PMID:9694845
- ↑ Kishko I, Carey J, Reha D, Brynda J, Winkler R, Harish B, Guerra R, Ettrichova O, Kukacka Z, Sheryemyetyeva O, Novak P, Kuty M, Kuta Smatanova I, Ettrich R, Lapkouski M. 1.2 A resolution crystal structure of Escherichia coli WrbA holoprotein. Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1748-57. doi:, 10.1107/S0907444913017162. Epub 2013 Aug 15. PMID:23999298 doi:10.1107/S0907444913017162
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