Structural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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Structural Insight Into Bioremediation of Triphenylmethane Dyes by Citrobacter Sp. Triphenylmethane Reductase

Kim, M.H.Kim, Y.Park, H.J.Lee, J.S.Kwak, S.N.Jung, W.H.Lee, S.G.Kim, D.Lee, Y.C.Oh, T.K.

(2008) J Biol Chem 283: 31981

  • DOI: https://doi.org/10.1074/jbc.M804092200
  • Primary Citation of Related Structures:  
    2JL1, 2VRB, 2VRC

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806. mhk8n@kribb.re.kr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIPHENYLMETHANE REDUCTASE287Citrobacter sp. MY-5Mutation(s): 0 
Find proteins for Q2TNI4 (Citrobacter sp. MY-5)
Explore Q2TNI4 
Go to UniProtKB:  Q2TNI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TNI4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.262α = 90
b = 140.384β = 90
c = 76.096γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description