2XH9

Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway.

Valegard, K., Iqbal, A., Kershaw, N.J., Ivison, D., Genereux, C., Dubus, A., Blikstad, C., Demetriades, M., Hopkinson, R.J., Lloyd, A.J., Roper, D.I., Schofield, C.J., Andersson, I., McDonough, M.A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1567-1579

  • DOI: 10.1107/S0907444913011013
  • Primary Citation of Related Structures:  
    2XEP, 2XF3, 2XFS, 2XFT, 2XH9, 2XGN

  • PubMed Abstract: 

    • Structural and biochemical studies of the orf12 gene product (ORF12) from the clavulanic acid (CA) biosynthesis gene cluster are described. Sequence and crystallographic analyses reveal two domains: a C-terminal penicillin-binding protein (PBP)/β-lactamase-type fold with highest structural similarity to the class A β-lactamases fused to an N-terminal domain with a fold similar to steroid isomerases and polyketide cyclases ...

    Structural and biochemical studies of the orf12 gene product (ORF12) from the clavulanic acid (CA) biosynthesis gene cluster are described. Sequence and crystallographic analyses reveal two domains: a C-terminal penicillin-binding protein (PBP)/β-lactamase-type fold with highest structural similarity to the class A β-lactamases fused to an N-terminal domain with a fold similar to steroid isomerases and polyketide cyclases. The C-terminal domain of ORF12 did not show β-lactamase or PBP activity for the substrates tested, but did show low-level esterase activity towards 3'-O-acetyl cephalosporins and a thioester substrate. Mutagenesis studies imply that Ser173, which is present in a conserved SXXK motif, acts as a nucleophile in catalysis, consistent with studies of related esterases, β-lactamases and D-Ala carboxypeptidases. Structures of wild-type ORF12 and of catalytic residue variants were obtained in complex with and in the absence of clavulanic acid. The role of ORF12 in clavulanic acid biosynthesis is unknown, but it may be involved in the epimerization of (3S,5S)-clavaminic acid to (3R,5R)-clavulanic acid.

    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, S-751 24 Uppsala, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF12A, B458Streptomyces clavuligerusMutation(s): 1 
UniProt
Find proteins for Q8KRB7 (Streptomyces clavuligerus)
Explore Q8KRB7 
Go to UniProtKB:  Q8KRB7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J01
Query on J01
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A], E [auth B], F [auth B](2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
C8 H9 N O5
HZZVJAQRINQKSD-PBFISZAISA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.514α = 90
b = 100.895β = 93.94
c = 81.355γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references, Version format compliance
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Database references