4OJ8 | pdb_00004oj8

Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics.

Chang, W.C.Guo, Y.Wang, C.Butch, S.E.Rosenzweig, A.C.Boal, A.K.Krebs, C.Bollinger, J.M.

(2014) Science 343: 1140-1144

  • DOI: https://doi.org/10.1126/science.1248000
  • Primary Citation Related Structures: 
    4OJ8

  • PubMed Abstract: 

    The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.


  • Organizational Affiliation
    • Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.

Macromolecule Content 

  • Total Structure Weight: 102.47 kDa 
  • Atom Count: 6,991 
  • Modeled Residue Count: 795 
  • Deposited Residue Count: 879 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
(5R)-carbapenem-3-carboxylate synthase
A, B, C
293Pectobacterium carotovorum subsp. carotovorumMutation(s): 0 
Gene Names: carC
EC: 1.14.20.3
UniProt
Find proteins for Q9XB59 (Pectobacterium carotovorum subsp. carotovorum)
Explore Q9XB59 
Go to UniProtKB:  Q9XB59
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XB59
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2TQ

Query on 2TQ



Download:Ideal Coordinates CCD File
I [auth B],
L [auth C]
(2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
C7 H9 N O3
RJPDELAUUYAFTQ-WHFBIAKZSA-N
AKG

Query on AKG



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
K [auth C]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
D [auth A],
F [auth B],
J [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.251α = 90
b = 165.778β = 90
c = 146.58γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description