1HJF

Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Alteration of the 2-Oxoacid Cosubstrate Selectivity in Deacetoxycephalosporin C Synthase: The Role of Arginine-258

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

(2001) J Biol Chem 276: 18290

  • DOI: https://doi.org/10.1074/jbc.M100085200
  • Primary Citation of Related Structures:  
    1HJF, 1HJG

  • PubMed Abstract: 

    Deacetoxycephalosporin C synthase is an iron(II) 2-oxoglutaratedependent oxygenase that catalyzes the oxidative ring-expansion of penicillin N to deacetoxycephalosporin C. The wild-type enzyme is only able to efficiently utilize 2-oxoglutarate and 2-oxoadipate as a 2-oxoacid co-substrate. Mutation of arginine 258, the side chain of which forms an electrostatic interaction with the 5-carboxylate of the 2-oxoglutarate co-substrate, to a glutamine residue reduced activity to about 5% of the wild-type enzyme with 2-oxoglutarate. However, other aliphatic 2-oxoacids, which were not co-substrates for the wild-type enzyme, were utilized by the R258Q mutant. These 2-oxoacids "rescued" catalytic activity to the level observed for the wild-type enzyme as judged by penicillin N and G conversion. These co-substrates underwent oxidative decarboxylation as observed for 2-oxoglutarate in the normal reaction with the wild-type enzyme. Crystal structures of the iron(II)- 2-oxo-3-methylbutanoate (1.5 A), and iron(II)-2-oxo-4-methylpentanoate (1.6 A) enzyme complexes were obtained, which reveal the molecular basis for this "chemical co-substrate rescue" and help to rationalize the co-substrate selectivity of 2-oxoglutaratedependent oxygenases.


  • Organizational Affiliation

    Oxford Centre for Molecular Sciences and the Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QY, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEACETOXYCEPHALOSPORIN C SYNTHASE311Streptomyces clavuligerusMutation(s): 1 
Gene Names: CEFER258Q MUTANT
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COI
Query on COI

Download Ideal Coordinates CCD File 
C [auth A]2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.933α = 90
b = 106.933β = 90
c = 70.819γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-01
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Atomic model, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description