1NX8

Structure of carbapenem synthase (CarC) complexed with N-acetyl proline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M213054200
  • Primary Citation of Related Structures:  1NX4

  • 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 wit ...

    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.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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


    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
MoleculeChainsSequence LengthOrganismDetails
Carbapenem synthase
A, B, C
273Pectobacterium carotovorum subsp. carotovorumGene Names: carC
EC: 1.14.20.3
Find proteins for Q9XB59 (Pectobacterium carotovorum subsp. carotovorum)
Go to UniProtKB:  Q9XB59
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N7P
Query on N7P

Download SDF File 
Download CCD File 
B, C
1-ACETYL-L-PROLINE
N-ACETYLPROLINE
C7 H11 N O3
GNMSLDIYJOSUSW-LURJTMIESA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B, C
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.443α = 90.00
b = 164.082β = 90.00
c = 146.330γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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
  • Version 1.3: 2012-07-11
    Type: Non-polymer description
  • Version 1.4: 2016-08-17
    Type: Non-polymer description