1Q19

Carbapenam Synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Carbapenam Synthetase (CarA)

Miller, M.T.Gerratana, B.Stapon, A.Townsend, C.A.Rosenzweig, A.C.

(2003) J.Biol.Chem. 278: 40996-41002

  • DOI: 10.1074/jbc.M307901200
  • Primary Citation of Related Structures:  1Q15

  • PubMed Abstract: 
  • Carbapenam synthetase (CarA) is an ATP/Mg2+-dependent enzyme that catalyzes formation of the beta-lactam ring in (5R)-carbapenem-3-carboxylic acid biosynthesis. CarA is homologous to beta-lactam synthetase (beta-LS), which is involved in clavulanic a ...

    Carbapenam synthetase (CarA) is an ATP/Mg2+-dependent enzyme that catalyzes formation of the beta-lactam ring in (5R)-carbapenem-3-carboxylic acid biosynthesis. CarA is homologous to beta-lactam synthetase (beta-LS), which is involved in clavulanic acid biosynthesis. The catalytic cycles of CarA and beta-LS mediate substrate adenylation followed by beta-lactamization via a tetrahedral intermediate or transition state. Another member of this family of ATP/Mg2+-dependent enzymes, asparagine synthetase (AS-B), catalyzes intermolecular, rather than intramolecular, amide bond formation in asparagine biosynthesis. The crystal structures of apo-CarA and CarA complexed with the substrate (2S,5S)-5-carboxymethylproline (CMPr), ATP analog alpha,beta-methyleneadenosine 5'-triphosphate (AMP-CPP), and a single Mg2+ ion have been determined. CarA forms a tetramer. Each monomer resembles beta-LS and AS-B in overall fold, but key differences are observed. The N-terminal domain lacks the glutaminase active site found in AS-B, and an extended loop region not observed in beta-LS or AS-B is present. Comparison of the C-terminal synthetase active site to that in beta-LS reveals that the ATP binding site is highly conserved. By contrast, variations in the substrate binding pocket reflect the different substrates of the two enzymes. The Mg2+ coordination is also different. Several key residues in the active site are conserved between CarA and beta-LS, supporting proposed roles in beta-lactam formation. These data provide further insight into the structures of this class of enzymes and suggest that CarA might be a versatile target for protein engineering experiments aimed at developing improved production methods and new carbapenem antibiotics.


    Organizational Affiliation

    Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CarA
A, B, C, D
503Pectobacterium carotovorum subsp. carotovorumGene Names: carA
EC: 6.3.3.6
Find proteins for Q9XB61 (Pectobacterium carotovorum subsp. carotovorum)
Go to UniProtKB:  Q9XB61
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download SDF File 
Download CCD File 
A, B, C, D
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
SSC
Query on SSC

Download SDF File 
Download CCD File 
A, B, C, D
(2S,5S)-5-CARBOXYMETHYLPROLINE
C7 H11 N O4
LIZWYFXJOOUDNV-WHFBIAKZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 103.042α = 90.00
b = 61.951β = 97.01
c = 175.870γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance