1NX4 | pdb_00001nx4

The crystal structure of carbapenem synthase (CarC)

• PDB DOI: https://doi.org/10.2210/pdb1NX4/pdb

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


• 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: 2.40 Å
• R-Value Free: 
  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

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 Biological Chem 278: 20843-20850

• PubMed: 12611886 
• DOI: https://doi.org/10.1074/jbc.M213054200
• Primary Citation Related Structures: 
  1NX4, 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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Organizational Affiliation: 
• Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.4 kDa 
• Atom Count: 6,348 
• Modeled Residue Count: 753 
• Deposited Residue Count: 819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem synthase	A, B, C	273	Pectobacterium carotovorum	Mutation(s): 6  Gene Names: CarC EC: 1.14.20.3
UniProt
Find proteins for Q9XB59 (Pectobacterium carotovorum subsp. carotovorum) Explore Q9XB59  Go to UniProtKB:  Q9XB59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	E [auth A], G [auth B], I [auth C]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE	D [auth A], F [auth B], H [auth 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: 2.40 Å
• R-Value Free:  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.93	α = 90
b = 163.946	β = 90
c = 146.455	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary