1VYR

Structure of pentaerythritol tetranitrate reductase complexed with picric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.140 
  • R-Value Observed: 0.100 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic Resolution Structures and Solution Behavior of Enzyme-Substrate Complexes of Enterobacter Cloacae Pb2 Pentaerythritol Tetranitrate Reductase: Multiple Conformational States and Implications for the Mechanism of Nitroaromatic Explosive Degradation

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

(2004) J Biol Chem 279: 30563

  • DOI: 10.1074/jbc.M403541200
  • Primary Citation of Related Structures:  
    1VYS, 1VYR, 1VYP

  • PubMed Abstract: 
  • The structure of pentaerythritol tetranitrate (PETN) reductase in complex with the nitroaromatic substrate picric acid determined previously at 1.55 A resolution indicated additional electron density between the indole ring of residue Trp-102 and the ...

    The structure of pentaerythritol tetranitrate (PETN) reductase in complex with the nitroaromatic substrate picric acid determined previously at 1.55 A resolution indicated additional electron density between the indole ring of residue Trp-102 and the nitro group at C-6 of picrate. The data suggested the presence of an unusual bond between substrate and the tryptophan side chain. Herein, we have extended the resolution of the PETN reductase-picric acid complex to 0.9 A. This high-resolution analysis indicates that the active site is partially occupied with picric acid and that the anomalous density seen in the original study is attributed to the population of multiple conformational states of Trp-102 and not a formal covalent bond between the indole ring of Trp-102 and picric acid. The significance of any interaction between Trp-102 and nitroaromatic substrates was probed further in solution and crystal complexes with wild-type and mutant (W102Y and W102F) enzymes. Unlike with wild-type enzyme, in the crystalline form picric acid was bound at full occupancy in the mutant enzymes, and there was no evidence for multiple conformations of active site residues. Solution studies indicate tighter binding of picric acid in the active sites of the W102Y and W102F enzymes. Mutation of Trp-102 does not impair significantly enzyme reduction by NADPH, but the kinetics of decay of the hydride-Meisenheimer complex are accelerated in the mutant enzymes. The data reveal that decay of the hydride-Meisenheimer complex is enzyme catalyzed and that the final distribution of reaction products for the mutant enzymes is substantially different from wild-type enzyme. Implications for the mechanism of high explosive degradation by PETN reductase are discussed.


    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
    • Crystallisation and Preliminary Diffraction Studies of Pentaerythritol Reductase from Enterobacter Cloacae Pb2
      Moody, P.C.E., Shikotra, N., French, C.E., Bruce, N.C., Scrutton, N.S.
      (1998) Acta Crystallogr D Biol Crystallogr D54: 675

    Organizational Affiliation

    Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENTAERYTHRITOL TETRANITRATE REDUCTASEA364Enterobacter cloacaeMutation(s): 0 
Gene Names: onr
Find proteins for P71278 (Enterobacter cloacae)
Explore P71278 
Go to UniProtKB:  P71278
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Download CCD File 
A
PICRIC ACID
C6 H3 N3 O7
OXNIZHLAWKMVMX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TNFKd:  5400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.140 
  • R-Value Observed: 0.100 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.979α = 90
b = 69.058β = 90
c = 89.121γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2014-08-13
    Changes: Atomic model, Other