4OJ8

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 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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This is version 1.1 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: 10.1126/science.1248000
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
(5R)-carbapenem-3-carboxylate synthaseA, B, C293Pectobacterium 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • 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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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