2vrb: Difference between revisions

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-{{Seed}}
-[[Image:2vrb.png|left|200px]]
-<!--
+==Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)==
-The line below this paragraph, containing "STRUCTURE_2vrb", creates the "Structure Box" on the page.
+<StructureSection load='2vrb' size='340' side='right'caption='[[2vrb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vrb]] is a 1 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=2VRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VRB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-{{STRUCTURE_2vrb|  PDB=2vrb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrb OCA], [https://pdbe.org/2vrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vrb RCSB], [https://www.ebi.ac.uk/pdbsum/2vrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vrb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2TNI4_9ENTR Q2TNI4_9ENTR]
+== 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/2vrb_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=2vrb 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.
-===CRYSTAL STRUCTURE OF THE CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE COMPLEXED WITH NADP(H)===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18782772}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vrb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18782772 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18782772}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Citrobacter sp. MY-5]]
-VRB is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VRB OCA].
+[[Category: Large Structures]]
+[[Category: Kim MH]]
-==Reference==
+[[Category: Kim Y]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/18782772 18782772]
+[[Category: Kwak SN]]
-[[Category: Bacteria]]
+[[Category: Lee JS]]
-[[Category: Kim, M H.]]
+[[Category: Oh TK]]
-[[Category: Kim, Y.]]
+[[Category: Park HJ]]
-[[Category: Kwak, S N.]]
-[[Category: Lee, J S.]]
-[[Category: Oh, T K.]]
-[[Category: Park, H J.]]
-[[Category: Oxidoreductase]]
-[[Category: Reductase]]
-[[Category: Sdr family]]
-[[Category: Triphenylmethane reduction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 20 07:53:06 2008''