1E5I

DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and Crystallographic Studies on Deacetoxycephalosporin C Synthase (Daocs)

Lee, H.J.Lloyd, M.D.Harlos, K.Clifton, I.J.Baldwin, J.E.Schofield, C.J.

(2001) J Mol Biol 308: 937

  • DOI: 10.1006/jmbi.2001.4649
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Deacetoxycephalosporin C synthase (DAOCS) is an iron(II) and 2-oxoglutarate-dependent oxygenase that catalyzes the conversion of penicillin N to deacetoxycephalosporin C, the committed step in the biosynthesis of cephalosporin antibiotics. The crysta ...

    Deacetoxycephalosporin C synthase (DAOCS) is an iron(II) and 2-oxoglutarate-dependent oxygenase that catalyzes the conversion of penicillin N to deacetoxycephalosporin C, the committed step in the biosynthesis of cephalosporin antibiotics. The crystal structure of DAOCS revealed that the C terminus of one molecule is inserted into the active site of its neighbor in a cyclical fashion within a trimeric unit. This arrangement has hindered the generation of crystalline enzyme-substrate complexes. Therefore, we constructed a series of DAOCS mutants with modified C termini. Oxidation of 2-oxoglutarate was significantly uncoupled from oxidation of the penicillin substrate in certain truncated mutants. The extent of uncoupling varied with the number of residues deleted and the penicillin substrate used. Crystal structures were determined for the DeltaR306 mutant complexed with iron(II) and 2-oxoglutarate (to 2.10 A) and the DeltaR306A mutant complexed with iron(II), succinate and unhydrated carbon dioxide (to 1.96 A). The latter may mimic a product complex, and supports proposals for a metal-bound CO(2) intermediate during catalysis.


    Related Citations: 
    • Studies on the Active Site of Deacetoxycephalosporin C Synthase (Daocs)
      Lloyd, M.D., Lee, H.J., Harlos, K., Zhang, Z.-H., Baldwin, J.E., Schofield, C.J., Charnock, J.M., Garner, C.D., Hara, T., Terrwisscha Van Scheltinga, A.C., Valegard, K., Viklund, J.A.C., Hajdu, J., Andersson, I., Danielsson, A., Bhikhabhai, R.
      (1999) J Mol Biol 287: 943

    Organizational Affiliation

    The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, South Parks Road, Oxford, OX1 3QY, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEACETOXYCEPHALOSPORIN C SYNTHASE
A
306Streptomyces clavuligerusMutation(s): 0 
Gene Names: cefE
EC: 1.14.20.1
Find proteins for P18548 (Streptomyces clavuligerus)
Go to UniProtKB:  P18548
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.787α = 90
b = 105.787β = 90
c = 71.222γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-26
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance