1H60

Structure of Pentaerythritol Tetranitrate Reductase in complex with progesterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

  • DOI: 10.1006/jmbi.2001.4779
  • Primary Citation of Related Structures:  1H50, 1H51, 1H61, 1H62, 1H63
  • Also Cited By: 1GVO, 1GVQ, 1GVR, 1GVS, 1VYP, 1VYR, 1VYS

  • PubMed Abstract: 
  • Pentaerythritol tetranitrate reductase (PETN reductase) degrades high explosive molecules including nitrate esters, nitroaromatics and cyclic triazine compounds. The enzyme also binds a variety of cyclic enones, including steroids; some steroids act ...

    Pentaerythritol tetranitrate reductase (PETN reductase) degrades high explosive molecules including nitrate esters, nitroaromatics and cyclic triazine compounds. The enzyme also binds a variety of cyclic enones, including steroids; some steroids act as substrates whilst others are inhibitors. Understanding the basis of reactivity with cyclic enones requires structural information for the enzyme and key complexes formed with steroid substrates and inhibitors. The crystal structure of oxidised and reduced PETN reductase at 1.5 A resolution establishes a close structural similarity to the beta/alpha-barrel flavoenzyme, old yellow enzyme. In complexes of oxidised PETN reductase with progesterone (an inhibitor), 1,4-androstadiene-3,17-dione and prednisone (both substrates) the steroids are stacked over the si-face of the flavin in an orientation different from that reported for old yellow enzyme. The specifically reducible 1,2 unsaturated bonds in 1,4-androstadiene-3,17-dione and prednisone are not optimally aligned with the flavin N5 in oxidised enzyme complexes. These structures suggest either relative "flipping" or shifting of the steroid with respect to the flavin when bound in different redox forms of the enzyme. Deuterium transfer from nicotinamide coenzyme to 1,4-androstadiene-3,17-dione via the enzyme bound FMN indicates 1alpha addition at the steroid C2 atom. These studies rule out lateral motion of the steroid and indicate that the steroid orientation is "flipped" in different redox states of the enzyme.


    Organizational Affiliation

    Department of Biochemistry, University of Leicester, Leicester, LE1 7RH, UK.




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
STR
Query on STR

Download SDF File 
Download CCD File 
A
PROGESTERONE
C21 H30 O2
RJKFOVLPORLFTN-LEKSSAKUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STRKd: 20000 nM BINDINGMOAD
STRKd: 20000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.686α = 90.00
b = 68.670β = 90.00
c = 88.664γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-05
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance