1CEF

CEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of cephalothin and cefotaxime to D-ala-D-ala-peptidase reveals a functional basis of a natural mutation in a low-affinity penicillin-binding protein and in extended-spectrum beta-lactamases.

Kuzin, A.P.Liu, H.Kelly, J.A.Knox, J.R.

(1995) Biochemistry 34: 9532-9540

  • Primary Citation of Related Structures:  1CEG

  • PubMed Abstract: 
  • Two clinically-important beta-lactam antibiotics, cephalothin and cefotaxime, have been observed by X-ray crystallography bound to the reactive Ser62 of the D-alanyl-D-alanine carboxypeptidase/transpeptidase of Streptomyces sp. R61. Refinement of the ...

    Two clinically-important beta-lactam antibiotics, cephalothin and cefotaxime, have been observed by X-ray crystallography bound to the reactive Ser62 of the D-alanyl-D-alanine carboxypeptidase/transpeptidase of Streptomyces sp. R61. Refinement of the two crystal structures produced R factors for 3 sigma (F) data of 0.166 (to 1.8 A) and 0.170 (to 2.0 A) for the cephalothin and cefotaxime complexes, respectively. In each complex, a water molecule is within 3.1 and 3.6 A of the acylated beta-lactam carbonyl carbon atom, but is poorly activated by active site residues for nucleophilic attack and deacylation. This apparent lack of good stereochemistry for facile hydrolysis is in accord with the long half-lives of cephalosporin intermediates in solution (20-40 h) and the efficacy of these beta-lactams as inhibitors of bacterial cell wall synthesis. Different hydrogen binding patterns of the two cephalosporins to Thr301 are consistent with the low cefotaxime affinity of an altered penicillin-binding protein, PBP-2x, reported in cefotaxime-resistant strains of Streptococcus pneumoniae, and with the ability of mutant class A beta-lactamases to hydrolyze third-generation cephalosporins.


    Related Citations: 
    • Crystallographic Mapping of Beta-Lactams Bound to a D-Alanyl-D-Alanine Peptidase Target Enzyme
      Kelly, J.A.,Knox, J.R.,Zhao, H.,Frere, J.M.,Ghaysen, J.M.
      (1989) J.Mol.Biol. 209: 281
    • 2.8-A Structure of Penicillin-Sensitive D-Alanyl Carboxypeptidase-Transpeptidase from Streptomyces R61 and Complexes with Beta-Lactams
      Kelly, J.A.,Knox, J.R.,Moews, P.C.,Hite, G.J.,Bartolone, J.B.,Zhao, H.,Joris, B.,Frere, J.M.,Ghuysen, J.M.
      (1985) J.Biol.Chem. 260: 6449
    • The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution
      Kelly, J.A.,Kuzin, A.P.
      (1995) J.Mol.Biol. 254: 223
    • On the Origin of Bacterial Resistance to Penicillin: Comparison of a Beta-Lactamase and a Penicillin Target
      Kelly, J.A.,Dideberg, O.,Charlier, P.,Wery, J.P.,Libert, M.,Moews, P.C.,Knox, J.R.,Duez, C.,Fraipont, C.,Joris, B.,al., et
      (1986) Science 231: 1429


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE
A
349Streptomyces sp. (strain R61)EC: 3.4.16.4
Find proteins for P15555 (Streptomyces sp. (strain R61))
Go to UniProtKB:  P15555
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CEF
Query on CEF

Download SDF File 
Download CCD File 
A
CEFOTAXIME, C3' cleaved, open, bound form
C14 H15 N5 O5 S2
NRYMPLKBKFIWQC-YVCCLBOHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.300α = 90.00
b = 67.300β = 90.00
c = 102.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
X-PLORmodel building
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance