1VYS

STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102Y MUTANT AND COMPLEXED WITH PICRIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 nitro group at C-6 of picrate ...

    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
    • 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 D Biol Crystallogr 54: 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 REDUCTASEA [auth X]364Enterobacter cloacaeMutation(s): 1 
Gene Names: onr
UniProt
Find proteins for P71278 (Enterobacter cloacae)
Explore P71278 
Go to UniProtKB:  P71278
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
B [auth X]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
TNF (Subject of Investigation/LOI)
Query on TNF

Download Ideal Coordinates CCD File 
C [auth X]PICRIC ACID
C6 H3 N3 O7
OXNIZHLAWKMVMX-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TNF Binding MOAD:  1VYS Kd: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.591α = 90
b = 68.33β = 90
c = 88.603γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-26
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.2: 2013-04-24
    Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.3: 2018-10-24
    Changes: Data collection, Source and taxonomy