1NU3

Limonene-1,2-epoxide hydrolase in complex with valpromide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site

Arand, M.Hallberg, B.M.Zou, J.Bergfors, T.Oesch, F.van der Werf, M.J.de Bont, J.A.M.Jones, T.A.Mowbray, S.L.

(2003) EMBO J. 22: 2583-2592

  • DOI: 10.1093/emboj/cdg275
  • Primary Citation of Related Structures:  1NWW

  • PubMed Abstract: 
  • Epoxide hydrolases are essential for the processing of epoxide-containing compounds in detoxification or metabolism. The classic epoxide hydrolases have an alpha/beta hydrolase fold and act via a two-step reaction mechanism including an enzyme-substr ...

    Epoxide hydrolases are essential for the processing of epoxide-containing compounds in detoxification or metabolism. The classic epoxide hydrolases have an alpha/beta hydrolase fold and act via a two-step reaction mechanism including an enzyme-substrate intermediate. We report here the structure of the limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis, solved using single-wavelength anomalous dispersion from a selenomethionine-substituted protein and refined at 1.2 A resolution. This enzyme represents a completely different structure and a novel one-step mechanism. The fold features a highly curved six-stranded mixed beta-sheet, with four alpha-helices packed onto it to create a deep pocket. Although most residues lining this pocket are hydrophobic, a cluster of polar groups, including an Asp-Arg-Asp triad, interact at its deepest point. Site-directed mutagenesis supports the conclusion that this is the active site. Further, a 1.7 A resolution structure shows the inhibitor valpromide bound at this position, with its polar atoms interacting directly with the residues of the triad. We suggest that several bacterial proteins of currently unknown function will share this structure and, in some cases, catalytic properties.


    Organizational Affiliation

    Department of Toxicology, University of Würzburg, Versbacher Strasse 9, D-97078 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
limonene-1,2-epoxide hydrolase
A, B
149Rhodococcus erythropolisGene Names: limA
EC: 3.3.2.8
Find proteins for Q9ZAG3 (Rhodococcus erythropolis)
Go to UniProtKB:  Q9ZAG3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VPR
Query on VPR

Download SDF File 
Download CCD File 
A, B
2-PROPYLPENTANAMIDE
VALPROMIDE
C8 H17 N O
OMOMUFTZPTXCHP-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VPRKi: 100000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.596α = 90.00
b = 47.656β = 90.00
c = 129.244γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
FFTphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance