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
  • Structures With Same Primary Citation

  • 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- ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEACETOXYCEPHALOSPORIN C SYNTHASE
A
311Streptomyces clavuligerusMutation(s): 1 
Gene Names: cefER258Q MUTANT
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
COI
Query on COI

Download CCD File 
A
2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-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: 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 

  • 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