5J8G

Structure of nitroreductase from E. cloacae complexed with para-nitrobenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase.

Pitsawong, W.Haynes, C.A.Koder, R.L.Rodgers, D.W.Miller, A.F.

(2017) Structure 25: 978-987.e4

  • DOI: 10.1016/j.str.2017.05.002
  • Primary Citation of Related Structures:  5J8D

  • PubMed Abstract: 
  • Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted┬ásynthesis. We solved crystal structures of NR c ...

    Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.


    Organizational Affiliation

    Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxygen-insensitive NAD(P)H nitroreductase
A, B, C, D
216Enterobacter cloacaeGene Names: nfsB (nfnB, nfsI)
EC: 1.-.-.-
Find proteins for Q01234 (Enterobacter cloacae)
Go to UniProtKB:  Q01234
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
4NB
Query on 4NB

Download SDF File 
Download CCD File 
A, B, C, D
4-NITROBENZOIC ACID
PARA NITROBENZOIC ACID
C7 H5 N O4
OTLNPYWUJOZPPA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.410α = 90.00
b = 113.440β = 101.55
c = 82.290γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS38401
National Science Foundation (United States)United StatesMCB 9904886
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM110787
National Science Foundation (United States)United StatesIIA-1355438

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2017-12-06
    Type: Database references