1H60

Structure of Pentaerythritol Tetranitrate Reductase in complex with progesterone

• PDB DOI:  https://doi.org/10.2210/pdb1H60/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-06-04 Released: 2001-07-05 
• Deposition Author(s): Barna, T.M., Moody, P.C.E.

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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 

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

• PubMed: 11428899 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.17 kDa 
• Atom Count: 3,499 
• Modelled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENTAERYTHRITOL TETRANITRATE REDUCTASE	A	364	Enterobacter cloacae	Mutation(s): 0  Gene Names: onr
UniProt
Find proteins for P71278 (Enterobacter cloacae) Explore P71278  Go to UniProtKB:  P71278

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
STR	C [auth A]	PROGESTERONE C21 H30 O2 RJKFOVLPORLFTN-LEKSSAKUSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 56.686	α = 90
b = 68.67	β = 90
c = 88.664	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-05 
Deposition Author(s): Barna, T.M., Moody, P.C.E.

Revision History  

• 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