Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 32.22 kDa 
• Atom Count: 2447 
• Residue Count: 287 
• Unique protein chains: 1

2JL1

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

• DOI: 10.2210/pdb2JL1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Citrobacter sp. MY-5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-02 Released: 2008-09-23 
• Deposition Author(s): Kim, Y., Park, H.J., Kwak, S.N., Kim, M.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.232 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

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

• PubMed: 18782772 
• DOI: 10.1074/jbc.M804092200
• Primary Citation of Related Structures:  
  2VRB, 2VRC, 2JL1


• 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIPHENYLMETHANE REDUCTASE	A	287	Citrobacter sp. MY-5	Mutation(s): 0
Find proteins for Q2TNI4 (Citrobacter sp. MY-5) Explore Q2TNI4  Go to UniProtKB:  Q2TNI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 59.262	α = 90
b = 140.384	β = 90
c = 76.096	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-02 
• Released Date: 2008-09-23 
Deposition Author(s): Kim, Y., Park, H.J., Kwak, S.N., Kim, M.H.

Revision History 

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance