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 1.3 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: 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 ...

    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.

    Related Citations: 
    • Studies on the Active Site of Deacetoxycephalosporin C Synthase
      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., Van Scheltinga, A.C.T., Valegard, K., Viklund, J.A.C., Hajdu, J., Andersson, I., Danielsson, A., Bhikhabhai, R.
      (1999) J Mol Biol 287: 943
    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
MoleculeChainsSequence LengthOrganismDetailsImage
DEACETOXYCEPHALOSPORIN C SYNTHASEA311Streptomyces clavuligerusMutation(s): 1 
Gene Names: cefE, R258Q MUTANT
EC: 1.14.20.1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
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

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View more in-depth experimental data

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