1RXF

DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.142 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1038/29575
  • Primary Citation of Related Structures:  
    1DCS, 1RXG, 1RXF

  • 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 ...

    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.


    Related Citations: 
    • Substrate Specificity of Recombinant Streptomyces Clavuligerus Deacetoxycephalosporin C Synthase
      Morgan, N., Pereira, I.A.C., Andersson, I., Adlington, R.M., Baldwin, J.E., Cole, S.E., Crouch, N.P., Sutherland, J.D.
      (1994) Bioorg Med Chem Lett 4: 1595

    Organizational Affiliation

    Department of Biochemistry, Uppsala University, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEACETOXYCEPHALOSPORIN C SYNTHASEA311Streptomyces clavuligerusMutation(s): 0 
Gene Names: cefE
EC: 1.14.20.1
UniProt
Find proteins for P18548 (Streptomyces clavuligerus)
Explore P18548 
Go to UniProtKB:  P18548
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.142 
  • R-Value Observed: 0.119 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.1α = 90
b = 106.1β = 90
c = 71.2γ = 120
Software Package:
Software NamePurpose
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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: Version format compliance