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| | ==Crystal structure of E. coli WrbA in complex with benzoquinone== | | ==Crystal structure of E. coli WrbA in complex with benzoquinone== |
| - | <StructureSection load='4yqe' size='340' side='right' caption='[[4yqe]], [[Resolution|resolution]] 1.33Å' scene=''> | + | <StructureSection load='4yqe' size='340' side='right'caption='[[4yqe]], [[Resolution|resolution]] 1.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yqe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YQE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YQE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yqe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YQE 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>, <scene name='pdbligand=PLQ:1,4-BENZOQUINONE'>PLQ</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]] 1.33Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</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=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=PLQ:1,4-BENZOQUINONE'>PLQ</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rg1|2rg1]], [[2r96|2r96]], [[2r97|2r97]], [[3zho|3zho]]</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=4yqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yqe OCA], [https://pdbe.org/4yqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yqe RCSB], [https://www.ebi.ac.uk/pdbsum/4yqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yqe ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yqe OCA], [http://pdbe.org/4yqe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yqe RCSB], [http://www.ebi.ac.uk/pdbsum/4yqe PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Brynda, J]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Carey, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Degtjarik, O]] | + | [[Category: Brynda J]] |
| - | [[Category: Ettrich, R]] | + | [[Category: Carey J]] |
| - | [[Category: Ettrichova, O]] | + | [[Category: Degtjarik O]] |
| - | [[Category: Smatanova, I Kuta]] | + | [[Category: Ettrich R]] |
| - | [[Category: Flavin mononucleotide]] | + | [[Category: Ettrichova O]] |
| - | [[Category: Oxidation-reduction]] | + | [[Category: Kuta Smatanova I]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Protein binding]]
| + | |
| - | [[Category: Repressor protein]]
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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
Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 A resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by approximately 5 A. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.
Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.,Degtjarik O, Brynda J, Ettrichova O, Kuty M, Sinha D, Kuta Smatanova I, Carey J, Ettrich R, Reha D J Phys Chem B. 2016 May 31. PMID:27183467[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
- ↑ Degtjarik O, Brynda J, Ettrichova O, Kuty M, Sinha D, Kuta Smatanova I, Carey J, Ettrich R, Reha D. Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA. J Phys Chem B. 2016 May 31. PMID:27183467 doi:http://dx.doi.org/10.1021/acs.jpcb.5b11958
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