1GVS

Structure of pentaerythritol tetranitrate reductase and complexed with picric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Kinetic and Structural Basis of Reactivity of Pentaerythritol Tetranitrate Reductase with Nadph,2-Cyclohexenone Nitroesters and Nitroaromatic Explosives

Khan, H.Harris, R.Barna, T.Craig, D.Bruce, N.Munro, A.Moody, P.C.E.Scrutton, N.

(2002) J.Biol.Chem. 277: 21906

  • DOI: 10.1074/jbc.M200637200
  • Primary Citation of Related Structures:  1GVO, 1GVQ, 1GVR

  • PubMed Abstract: 
  • The reaction of pentaerythritol tetranitrate reductase with reducing and oxidizing substrates has been studied by stopped-flow spectrophotometry, redox potentiometry, and X-ray crystallography. We show in the reductive half-reaction of pentaerythrito ...

    The reaction of pentaerythritol tetranitrate reductase with reducing and oxidizing substrates has been studied by stopped-flow spectrophotometry, redox potentiometry, and X-ray crystallography. We show in the reductive half-reaction of pentaerythritol tetranitrate (PETN) reductase that NADPH binds to form an enzyme-NADPH charge transfer intermediate prior to hydride transfer from the nicotinamide coenzyme to FMN. In the oxidative half-reaction, the two-electron-reduced enzyme reacts with several substrates including nitroester explosives (glycerol trinitrate and PETN), nitroaromatic explosives (trinitrotoluene (TNT) and picric acid), and alpha,beta-unsaturated carbonyl compounds (2-cyclohexenone). Oxidation of the flavin by the nitroaromatic substrate TNT is kinetically indistinguishable from formation of its hydride-Meisenheimer complex, consistent with a mechanism involving direct nucleophilic attack by hydride from the flavin N5 atom at the electron-deficient aromatic nucleus of the substrate. The crystal structures of complexes of the oxidized enzyme bound to picric acid and TNT are consistent with direct hydride transfer from the reduced flavin to nitroaromatic substrates. The mode of binding the inhibitor 2,4-dinitrophenol (2,4-DNP) is similar to that observed with picric acid and TNT. In this position, however, the aromatic nucleus is not activated for hydride transfer from the flavin N5 atom, thus accounting for the lack of reactivity with 2,4-DNP. Our work with PETN reductase establishes further a close relationship to the Old Yellow Enzyme family of proteins but at the same time highlights important differences compared with the reactivity of Old Yellow Enzyme. Our studies provide a structural and mechanistic rationale for the ability of PETN reductase to react with the nitroaromatic explosive compounds TNT and picric acid and for the inhibition of enzyme activity with 2,4-DNP.


    Related Citations: 
    • Crystal Structure of Pentaerythritol Tetranitrate Reductase: "Flipped" Binding Geometries for Steroid Substrates in Different Redox States of the Enzyme
      Barna, T.M.,Khan, H.,Bruce, N.C.,Barsukov, I.,Scrutton, N.S.,Moody, P.C.
      (2001) J.Mol.Biol. 310: 433
    • Crystallization and Preliminary Diffraction Studies of Pentaerythritol Tetranitrate Reductase from Enterobacter Cloacae Pb2.
      Moody, P.C.E.,Shikotra, N.,French, C.E.,Bruce, N.C.,Scrutton, N.S.
      (1998) Acta Crystallogr.,Sect.D 54: 675


    Organizational Affiliation

    Department of Biochemistry and Centre for Chemical Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENTAERYTHRITOL TETRANITRATE REDUCTASE
A
364Enterobacter cloacaeGene Names: onr
Find proteins for P71278 (Enterobacter cloacae)
Go to UniProtKB:  P71278
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
TNF
Query on TNF

Download SDF File 
Download CCD File 
A
PICRIC ACID
2,4,6-TRINITROPHENOL
C6 H3 N3 O7
OXNIZHLAWKMVMX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.963α = 90.00
b = 69.094β = 90.00
c = 89.024γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-27
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.2: 2013-05-01
    Type: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.3: 2017-03-29
    Type: Structure summary