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< | ==Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)== | ||
<StructureSection load='2vrc' size='340' side='right'caption='[[2vrc]], [[Resolution|resolution]] 2.50Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2vrc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_sp._my-5 Citrobacter sp. my-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VRC FirstGlance]. <br> | |||
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vrb|2vrb]]</div></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=2vrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrc OCA], [https://pdbe.org/2vrc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vrc RCSB], [https://www.ebi.ac.uk/pdbsum/2vrc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vrc ProSAT]</span></td></tr> | |||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vr/2vrc_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vrc ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Triphenylmethane dyes are aromatic xenobiotic compounds that are widely considered to be one of the main culprits of environmental pollution. Triphenylmethane reductase (TMR) from Citrobacter sp. strain KCTC 18061P was initially isolated and biochemically characterized as an enzyme that catalyzes the reduction of triphenylmethane dyes. Information from the primary amino acid sequence suggests that TMR is a dinucleotide-binding motif-containing enzyme; however, no other functional clues can be derived from sequence analysis. We present the crystal structure of TMR in complex with NADP+ at 2.0-angstroms resolution. Despite limited sequence similarity, the enzyme shows remarkable structural similarity to short-chain dehydrogenase/reductase (SDR) family proteins. Functional assignments revealed that TMR has features of both classic and extended SDR family members and does not contain a conserved active site. Thus, it constitutes a novel class of SDR family proteins. On the basis of simulated molecular docking using the substrate malachite green and the TMR/NADP+ crystal structure, together with site-directed mutagenesis, we have elucidated a potential molecular mechanism for triphenylmethane dye reduction. | |||
Structural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase.,Kim MH, Kim Y, Park HJ, Lee JS, Kwak SN, Jung WH, Lee SG, Kim D, Lee YC, Oh TK J Biol Chem. 2008 Nov 14;283(46):31981-90. Epub 2008 Sep 9. PMID:18782772<ref>PMID:18782772</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vrc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Citrobacter sp. my-5]] | ||
[[Category: Large Structures]] | |||
[[Category: Kim, M H]] | |||
== | [[Category: Kim, Y]] | ||
[[Category: Kwak, S N]] | |||
[[Category: | [[Category: Lee, J S]] | ||
[[Category: | [[Category: Oh, T K]] | ||
[[Category: Kim, M H | [[Category: Park, H J]] | ||
[[Category: Kim, Y | |||
[[Category: Kwak, S N | |||
[[Category: Lee, J S | |||
[[Category: Oh, T K | |||
[[Category: Park, H J | |||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
[[Category: Reductase]] | [[Category: Reductase]] | ||
[[Category: Sdr family]] | [[Category: Sdr family]] | ||
[[Category: Triphenylmethane reduction]] | [[Category: Triphenylmethane reduction]] | ||
Latest revision as of 14:44, 30 March 2022
Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)
Structural highlights
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 PubMedTriphenylmethane dyes are aromatic xenobiotic compounds that are widely considered to be one of the main culprits of environmental pollution. Triphenylmethane reductase (TMR) from Citrobacter sp. strain KCTC 18061P was initially isolated and biochemically characterized as an enzyme that catalyzes the reduction of triphenylmethane dyes. Information from the primary amino acid sequence suggests that TMR is a dinucleotide-binding motif-containing enzyme; however, no other functional clues can be derived from sequence analysis. We present the crystal structure of TMR in complex with NADP+ at 2.0-angstroms resolution. Despite limited sequence similarity, the enzyme shows remarkable structural similarity to short-chain dehydrogenase/reductase (SDR) family proteins. Functional assignments revealed that TMR has features of both classic and extended SDR family members and does not contain a conserved active site. Thus, it constitutes a novel class of SDR family proteins. On the basis of simulated molecular docking using the substrate malachite green and the TMR/NADP+ crystal structure, together with site-directed mutagenesis, we have elucidated a potential molecular mechanism for triphenylmethane dye reduction. Structural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase.,Kim MH, Kim Y, Park HJ, Lee JS, Kwak SN, Jung WH, Lee SG, Kim D, Lee YC, Oh TK J Biol Chem. 2008 Nov 14;283(46):31981-90. Epub 2008 Sep 9. PMID:18782772[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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