Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96399.52 
• Atom Count: 6105 
• Residue Count: 819 
• Unique protein chains: 1

1NX4

The crystal structure of carbapenem synthase (CarC)

• DOI: 10.2210/pdb1NX4/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pectobacterium carotovorum subsp. carotovorum
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-02-08 Released: 2003-06-17 
• Deposition Author(s): Clifton, I.J., Doan, L.X., Sleeman, M.C., Topf, M., Suzuki, H., Wilmouth, R.C., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.268 
• R-Value Work: 0.221 

Literature

Crystal structure of carbapenem synthase (CarC).

Clifton, I.J., Doan, L.X., Sleeman, M.C., Topf, M., Suzuki, H., Wilmouth, R.C., Schofield, C.J.

(2003) J.Biol.Chem. 278: 20843-20850

• PubMed: 12611886 
• DOI: 10.1074/jbc.M213054200
• Primary Citation of Related Structures:  
  1NX8


• PubMed Abstract: 
  

The proposed biosynthetic pathway to the carbapenem antibiotics proceeds via epimerization/desaturation of a carbapenam in an unusual process catalyzed by an iron- and 2-oxoglutarate-dependent oxygenase, CarC. Crystal structures of CarC complexed with Fe(II) and 2-oxoglutarate reveal it to be hexameric (space group C2221), consistent with solution studies. CarC monomers contain a double-stranded beta-helix core that supports ligands binding a single Fe(II) to which 2-oxoglutarate complexes in a bi-dentate manner. A structure was obtained with l-N-acetylproline acting as a substrate analogue. Quantum mechanical/molecular mechanical modeling studies with stereoisomers of carbapenams and carbapenems were used to investigate substrate binding. The combined work will stimulate further mechanistic studies and aid in the engineering of carbapenem biosynthesis.

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Related Citations: 

• A Chiral Synthesis of trans-Carbapenam-3-carboxylic Acid and the Assignment of (3S, 5S) Configuration to the Corresponding Product from Serratia and Erwinia Species.
  Bycroft, B.W.,Chhabra, S.R.
  (1989) J.CHEM.SOC.,CHEM.COMMUN. --: 423
• Bacterial production of carbapenems and clavams: evolution of beta-lactam antibiotic pathways
  McGowan, S.J.,Bycroft, B.W.,Salmond, G.P.C.
  (1998) Trends Microbiol. 6: 203
• Analysis of the carbapenem gene cluster of Erwinia carotovora: definition of the antibiotic biosynthetic genes and evidence for a novel beta-lactam resistance mechanism
  McGowan, S.J.,Sebaihia, M.,O'Leary, S.,Hardie, K.R.,Williams, P.,Stewart, G.S.A.B.,Bycroft, B.W.,Salmond, G.P.C.
  (1997) MOL.MICROBIOL. 26: 545
• Three Unusual Reactions Mediate Carbapenem and Carbapenam Biosynthesis
  Li, R.,Stapon, A.,Blanchfield, J.T.,Townsend, C.A.
  (2000) J.AM.CHEM.SOC. 122: 9296
• Diastereoselective synthesis of 3,5-trans-(+)-(3R,5R)-3- carbomethoxycarbapenam from 3-hydroxypyridine: questioning the stereochemical assignment of the natural product
  Tanaka, H.,Sakagami, H.,Ogasawara, K.
  (2002) TETRAHEDRON LETT. 43: 93




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbapenem synthase	A, B, C	273	Pectobacterium carotovorum subsp. carotovorum	Mutation(s): 0  Gene Names: carC EC: 1.14.20.3
Find proteins for Q9XB59 (Pectobacterium carotovorum subsp. carotovorum) Go to UniProtKB:  Q9XB59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
AKG	A, B, C	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE	A, B, C	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.268 
• R-Value Work: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 79.930	α = 90.00
b = 163.946	β = 90.00
c = 146.455	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
MOSFLM	data reduction
REFMAC	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-08 
• Released Date: 2003-06-17 
• Deposition Author(s): Clifton, I.J., Doan, L.X., Sleeman, M.C., Topf, M., Suzuki, H., Wilmouth, R.C., Schofield, C.J.

Revision History 

• Version 1.0: 2003-06-17
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance