3BM1

Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor

Choi, J.-W.Lee, J.Nishi, K.Kim, Y.-S.Jung, C.-H.Kim, J.-S.

(2008) J.Mol.Biol. 377: 258-267

  • DOI: 10.1016/j.jmb.2008.01.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal stru ...

    Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal structures of ydjA from Escherichia coli (Ec_ydjA), one of the smallest NTRs, in its flavin mononucleotide (FMN)-bound and cofactor-free forms. The alpha+beta mixed monomeric Ec_ydjA forms a homodimeric structure through the interactions of the long central helices and the extended regions at both termini. Two FMN molecules are bound at the dimeric interface. The absence of the 30 internal amino acids in Ec_ydjA, which forms two helices and restricts the cofactor and substrate binding in other NTR family members, creates a wider and more flexible active site. Unlike the bent FMN ring structures present in most NTR complexes currently known, the flavin system in the Ec_ydjA structure maintains a flat ring conformation, which is sandwiched between a Trp and a His residue from each monomer. The analysis of our Ec_ydjA structure explains its specificity for larger substrates and provides structural information for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.


    Organizational Affiliation

    Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ydjA
A, B
183Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ydjA
EC: 1.-.-.-
Find proteins for P0ACY1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACY1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.795α = 90.00
b = 77.645β = 90.00
c = 91.057γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-12-12 
  • Released Date: 2008-01-01 
  • Deposition Author(s): Choi, J.W., Kim, J.S.

Revision History 

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description