Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34748.56 
• Atom Count: 2157 
• Residue Count: 311 
• Unique protein chains: 1

1HJF

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

• DOI: 10.2210/pdb1HJF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2001-01-15 Released: 2001-06-01 
• Deposition Author(s): Lee, H.J., Lloyd, M.D., Clifton, I.J., Harlos, K., Dubus, A., Baldwin, J.E., Frere, J.M., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.269 
• R-Value Work: 0.241 

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

• PubMed: 11279000 
• DOI: 10.1074/jbc.M100085200
• Primary Citation of Related Structures:  
  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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
DEACETOXYCEPHALOSPORIN C SYNTHASE	A	311	Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602)	Mutation(s): 1  Gene Names: cefE EC: 1.14.20.1
Find proteins for P18548 (Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602)) Go to UniProtKB:  P18548

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
COI	A	2-OXO-4-METHYLPENTANOIC ACID alpha-ketoisocaproic acid C6 H10 O3 BKAJNAXTPSGJCU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.269 
• R-Value Work: 0.241 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 106.933	α = 90.00
b = 106.933	β = 90.00
c = 70.819	γ = 120.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
CNS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-15 
• Released Date: 2001-06-01 
• Deposition Author(s): Lee, H.J., Lloyd, M.D., Clifton, I.J., Harlos, K., Dubus, A., Baldwin, J.E., Frere, J.M., Schofield, C.J.

Revision History 

• Version 1.0: 2001-06-01
  Type: Initial release
• Version 1.1: 2013-07-24
  Type: Atomic model, Non-polymer description, Other, Version format compliance
• Version 1.2: 2018-10-24
  Type: Data collection, Source and taxonomy
• Version 1.3: 2019-05-08
  Type: Data collection, Experimental preparation