1H60

Structure of Pentaerythritol Tetranitrate Reductase in complex with progesterone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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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, 1H60, 1H61, 1H62, 1H63

  • 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 as substrates whilst others are inhibitors ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENTAERYTHRITOL TETRANITRATE REDUCTASEA364Enterobacter cloacaeMutation(s): 0 
Gene Names: onr
UniProt
Find proteins for P71278 (Enterobacter cloacae)
Explore P71278 
Go to UniProtKB:  P71278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71278
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 Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
STR
Query on STR
Download Ideal Coordinates CCD File 
C [auth A]PROGESTERONE
C21 H30 O2
RJKFOVLPORLFTN-LEKSSAKUSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
STR Binding MOAD:  1H60 Kd: 2.00e+4 (nM) from 1 assay(s)
PDBBind:  1H60 Kd: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.686α = 90
b = 68.67β = 90
c = 88.664γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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