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| | ==Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor== | | ==Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor== |
| - | <StructureSection load='3bp1' size='340' side='right' caption='[[3bp1]], [[Resolution|resolution]] 1.53Å' scene=''> | + | <StructureSection load='3bp1' size='340' side='right'caption='[[3bp1]], [[Resolution|resolution]] 1.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bp1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibch Vibch]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BP1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BP1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3bp1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O1_biovar_El_Tor_str._N16961 Vibrio cholerae O1 biovar El Tor str. N16961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BP1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 1.53Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">queF, VC_0902 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243277 VIBCH])</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=3bp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bp1 OCA], [https://pdbe.org/3bp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bp1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bp1 ProSAT], [https://www.topsan.org/Proteins/MCSG/3bp1 TOPSAN]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.13 1.7.1.13] </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=3bp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bp1 OCA], [http://pdbe.org/3bp1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bp1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bp1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bp1 ProSAT], [http://www.topsan.org/Proteins/MCSG/3bp1 TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/QUEF_VIBCH QUEF_VIBCH] Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/3bp1_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/3bp1_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Oxidoreductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Vibch]] | + | [[Category: Vibrio cholerae O1 biovar El Tor str. N16961]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Kim, Y]] | + | [[Category: Kim Y]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Moy S]] |
| - | [[Category: Moy, S]] | + | [[Category: Zhou M]] |
| - | [[Category: Zhou, M]] | + | |
| - | [[Category: Alpha-beta structure]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| Structural highlights
3bp1 is a 4 chain structure with sequence from Vibrio cholerae O1 biovar El Tor str. N16961. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.53Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
QUEF_VIBCH Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) (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
Here, we report the 1.53-A crystal structure of the enzyme 7-cyano-7-deazaguanine reductase (QueF) from Vibrio cholerae, which is responsible for the complete reduction of a nitrile (CN) bond to a primary amine (H(2)C-NH(2)). At present, this is the only example of a biological pathway that includes reduction of a nitrile bond, establishing QueF as particularly noteworthy. The structure of the QueF monomer resembles two connected ferrodoxin-like domains that assemble into dimers. Ligands identified in the crystal structure suggest the likely binding conformation of the native substrates NADPH and 7-cyano-7-deazaguanine. We also report on a series of numerical simulations that have shed light on the mechanism by which this enzyme affects the transfer of four protons (and electrons) to the 7-cyano-7-deazaguanine substrate. In particular, the simulations suggest that the initial step of the catalytic process is the formation of a covalent adduct with the residue Cys194, in agreement with previous studies. The crystal structure also suggests that two conserved residues (His233 and Asp102) play an important role in the delivery of a fourth proton to the substrate.
High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism.,Kim Y, Zhou M, Moy S, Morales J, Cunningham MA, Joachimiak A J Mol Biol. 2010 Nov 19;404(1):127-37. Epub 2010 Sep 25. PMID:20875425[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kim Y, Zhou M, Moy S, Morales J, Cunningham MA, Joachimiak A. High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. J Mol Biol. 2010 Nov 19;404(1):127-37. Epub 2010 Sep 25. PMID:20875425 doi:http://dx.doi.org/10.1016/j.jmb.2010.09.042
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