1RXG

DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) AND 2-OXOGLUTARATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.156 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a cephalosporin synthase.

Valegard, K.van Scheltinga, A.C.Lloyd, M.D.Hara, T.Ramaswamy, S.Perrakis, A.Thompson, A.Lee, H.J.Baldwin, J.E.Schofield, C.J.Hajdu, J.Andersson, I.

(1998) Nature 394: 805-809

  • DOI: https://doi.org/10.1038/29575
  • Primary Citation of Related Structures:  
    1DCS, 1RXF, 1RXG

  • PubMed Abstract: 

    Penicillins and cephalosporins are among the most widely used therapeutic agents. These antibiotics are produced from fermentation-derived materials as their chemical synthesis is not commercially viable. Unconventional steps in their biosynthesis are catalysed by Fe(II)-dependent oxidases/oxygenases; isopenicillin N synthase (IPNS) creates in one step the bicyclic nucleus of penicillins, and deacetoxycephalosporin C synthase (DAOCS) catalyses the expansion of the penicillin nucleus into the nucleus of cephalosporins. Both enzymes use dioxygen-derived ferryl intermediates in catalysis but, in contrast to IPNS, the ferryl form of DAOCS is produced by the oxidative splitting of a co-substrate, 2-oxoglutarate (alpha-ketoglutarate). This route of controlled ferryl formation and reaction is common to many mononuclear ferrous enzymes, which participate in a broader range of reactions than their well-characterized counterparts, the haem enzymes. Here we report the first crystal structure of a 2-oxoacid-dependent oxygenase. High-resolution structures for apo-DAOCS, the enzyme complexed with Fe(II), and with Fe(II) and 2-oxoglutarate, were obtained from merohedrally twinned crystals. Using a model based on these structures, we propose a mechanism for ferryl formation.


  • Organizational Affiliation

    Department of Biochemistry, Uppsala University, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEACETOXYCEPHALOSPORIN C SYNTHASE311Streptomyces clavuligerusMutation(s): 0 
UniProt
Find proteins for P18548 (Streptomyces clavuligerus)
Explore P18548 
Go to UniProtKB:  P18548
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18548
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.156 
  • R-Value Observed: 0.125 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.7α = 90
b = 107.7β = 90
c = 71γ = 120
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection, Other
  • Version 1.4: 2021-03-10
    Changes: Advisory, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references