1HL7

Gamma lactamase from an Aureobacterium species in complex with 3a,4,7,7a-tetrahydro-benzo [1,3] dioxol-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crystal Structure of a (-)Gamma-Lactamase from an Aureobacterium Species Reveals a Tetrahedral Intermediate in the Active Site

Line, K.Isupov, M.N.Littlechild, J.A.

(2004) J.Mol.Biol. 338: 519

  • DOI: 10.1016/j.jmb.2004.03.001
  • Primary Citation of Related Structures:  1HKH

  • PubMed Abstract: 
  • The structure of the recombinant (-) gamma-lactamase from an Aureobacterium species has been solved at 1.73A resolution in the cubic space group F23 with unit cell parameters a=b=c=240.6A. The trimeric enzyme has an alpha/beta hydrolase fold and clos ...

    The structure of the recombinant (-) gamma-lactamase from an Aureobacterium species has been solved at 1.73A resolution in the cubic space group F23 with unit cell parameters a=b=c=240.6A. The trimeric enzyme has an alpha/beta hydrolase fold and closely resembles the cofactor free haloperoxidases. The structure has been solved in complex with a covalently bound ligand originating from the host cell and also in the unligated form. The associated density in the former structure has been interpreted as the two-ring ligand (3aR,7aS)-3a,4,7,7a-tetrahydro-benzo [1,3] dioxol-2-one which forms a tetrahedral complex with OG of the catalytic Ser98. Soaks of these crystals with the industrial substrate gamma-lactam or its structural analogue, norcamphor, result in the displacement of the ligand from the enzyme active site, thereby allowing determination of the unligated structure. The presence of the ligand in the active site protects the enzyme from serine hydrolase inhibitors. Cyclic ethylene carbonate, the first ring of the ligand, was shown to be a substrate of the enzyme.


    Organizational Affiliation

    Exeter Biocatalysis Centre, School of Biological and Chemical Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA LACTAMASE
A, B
279uncultured Microbacterium sp.N/A
Find proteins for Q8GJP7 (uncultured Microbacterium sp.)
Go to UniProtKB:  Q8GJP7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BD1
Query on BD1

Download SDF File 
Download CCD File 
A, B
3A,4,7,7A-TETRAHYDRO-BENZO [1,3] DIOXOL-2-ONE
C7 H10 O3
VYBGCFNFGGLKAA-ZMONIFLSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.151 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 240.592α = 90.00
b = 240.592β = 90.00
c = 240.592γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance