3X21 | pdb_00003x21

Crystal structure of Escherichia coli nitroreductase NfsB mutant T41L/N71S/F124W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.256 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Altering the regioselectivity of a nitroreductase in the synthesis of arylhydroxylamines by structure-based engineering.

Bai, J.Zhou, Y.Chen, Q.Yang, Q.Yang, J.

(2015) Chembiochem 16: 1219-1225

  • DOI: https://doi.org/10.1002/cbic.201500070
  • Primary Citation Related Structures: 
    3X21

  • PubMed Abstract: 

    Nitroreductases have great potential for the highly efficient reduction of aryl nitro compounds to arylhydroxylamines. However, regioselective reduction of the desired nitro group in polynitroarenes is still a challenge. Here, we describe the structure-based engineering of Escherichia coli nitroreductase NfsB to alter its regioselectivity, in order to achieve reduction of a target nitro group. When 2,4-dinitrotoluene was used as the substrate, the wild-type enzyme regioselectively reduced the 4-NO2 group, but the T41L/N71S/F124W mutant primarily reduced the 2-NO2 group, without loss of activity. The crystal structure of T41L/N71S/F124W and docking experiments indicated that the regioselectivity change (from 4-NO2 to 2-NO2 ) might result from the increased hydrophobicity of residues 41 and 124 (proximal to FMN) and conformational changes in residues 70 and 124.


  • Organizational Affiliation
    • School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian-116023 (China).

Macromolecule Content 

  • Total Structure Weight: 265.89 kDa 
  • Atom Count: 17,176 
  • Modeled Residue Count: 2,170 
  • Deposited Residue Count: 2,370 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-insensitive NAD(P)H nitroreductase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
237Escherichia coli K-12Mutation(s): 3 
Gene Names: nfnBdprAnfsBnfsIntr
EC: 1.5.1.34 (PDB Primary Data), 1 (UniProt)
UniProt
Find proteins for P38489 (Escherichia coli (strain K12))
Explore P38489 
Go to UniProtKB:  P38489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38489
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
K [auth A]
L [auth B]
M [auth C]
N [auth D]
O [auth E]
K [auth A],
L [auth B],
M [auth C],
N [auth D],
O [auth E],
P [auth F],
Q [auth G],
R [auth H],
S [auth I],
T [auth J]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.256 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.41α = 90
b = 59.924β = 99.72
c = 220.063γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
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: 2015-05-20
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description