2vrb

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)

Structural highlights

2vrb is a 1 chain structure with sequence from Citrobacter sp. MY-5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q2TNI4_9ENTR

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

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kim MH, Kim Y, Park HJ, Lee JS, Kwak SN, Jung WH, Lee SG, Kim D, Lee YC, Oh TK. Structural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase. J Biol Chem. 2008 Nov 14;283(46):31981-90. Epub 2008 Sep 9. PMID:18782772 doi:10.1074/jbc.M804092200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vrb"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vrb' size='340' side='right'caption='[[2vrb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<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>
-</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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jl1|2jl1]], [[2vrc|2vrc]]</div></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>
 <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]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Citrobacter sp. my-5]]
+[[Category: Citrobacter sp. MY-5]]
 [[Category: Large Structures]]
-[[Category: Kim, M H]]
+[[Category: Kim MH]]
-[[Category: Kim, Y]]
+[[Category: Kim Y]]
-[[Category: Kwak, S N]]
+[[Category: Kwak SN]]
-[[Category: Lee, J S]]
+[[Category: Lee JS]]
-[[Category: Oh, T K]]
+[[Category: Oh TK]]
-[[Category: Park, H J]]
+[[Category: Park HJ]]
-[[Category: Oxidoreductase]]
-[[Category: Reductase]]
-[[Category: Sdr family]]
-[[Category: Triphenylmethane reduction]]

2vrb

From Proteopedia

Current revision

Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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