1E5I | pdb_00001e5i

DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE.

• PDB DOI: https://doi.org/10.2210/pdb1E5I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces clavuligerus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-07-26 Released: 2001-07-26 
• Deposition Author(s): Lee, H.J., Lloyd, M.D., Harlos, K., Clifton, I.J., Baldwin, J.E., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Kinetic and Crystallographic Studies on Deacetoxycephalosporin C Synthase (Daocs)

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

(2001) J Mol Biology 308: 937

• PubMed: 11352583 
• DOI: https://doi.org/10.1006/jmbi.2001.4649
• Primary Citation Related Structures: 
  1E5H, 1E5I


• PubMed Abstract: 
  

  Deacetoxycephalosporin C synthase (DAOCS) is an iron(II) and 2-oxoglutarate-dependent oxygenase that catalyzes the conversion of penicillin N to deacetoxycephalosporin C, the committed step in the biosynthesis of cephalosporin antibiotics. The crystal structure of DAOCS revealed that the C terminus of one molecule is inserted into the active site of its neighbor in a cyclical fashion within a trimeric unit. This arrangement has hindered the generation of crystalline enzyme-substrate complexes. Therefore, we constructed a series of DAOCS mutants with modified C termini. Oxidation of 2-oxoglutarate was significantly uncoupled from oxidation of the penicillin substrate in certain truncated mutants. The extent of uncoupling varied with the number of residues deleted and the penicillin substrate used. Crystal structures were determined for the DeltaR306 mutant complexed with iron(II) and 2-oxoglutarate (to 2.10 A) and the DeltaR306A mutant complexed with iron(II), succinate and unhydrated carbon dioxide (to 1.96 A). The latter may mimic a product complex, and supports proposals for a metal-bound CO(2) intermediate during catalysis.

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Organizational Affiliation: 
• The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, South Parks Road, Oxford, OX1 3QY, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.25 kDa 
• Atom Count: 2,211 
• Modeled Residue Count: 268 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEACETOXYCEPHALOSPORIN C SYNTHASE	A	306	Streptomyces clavuligerus	Mutation(s): 0  Gene Names: CEFE EC: 1.14.20.1
UniProt
Find proteins for P18548 (Streptomyces clavuligerus) Explore P18548  Go to UniProtKB:  P18548

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.787	α = 90
b = 105.787	β = 90
c = 71.222	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-26 
Deposition Author(s): Lee, H.J., Lloyd, M.D., Harlos, K., Clifton, I.J., Baldwin, J.E., Schofield, C.J.

Revision History  

• Version 1.0: 2001-07-26
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description