1PWD

Covalent acyl enzyme complex of the Streptomyces R61 DD-peptidase with cephalosporin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin"

Silvaggi, N.R.Josephine, H.R.Kuzin, A.P.Nagarajan, R.Pratt, R.F.Kelly, J.A.

(2005) J.Mol.Biol. 345: 521-533

  • DOI: 10.1016/j.jmb.2004.10.076
  • Primary Citation of Related Structures:  1PW1, 1PW8, 1PWC, 1PWG

  • PubMed Abstract: 
  • The bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases) are the killing targets of beta-lactams, the most important clinical defense against bacterial infections. However, due to the constant development of antibiotic-resistance mechanisms b ...

    The bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases) are the killing targets of beta-lactams, the most important clinical defense against bacterial infections. However, due to the constant development of antibiotic-resistance mechanisms by bacteria, there is an ever-present need for new, more effective antimicrobial drugs. While enormous numbers of beta-lactam compounds have been tested for antibiotic activity in over 50 years of research, the success of a beta-lactam structure in terms of antibiotic activity remains unpredictable. Tipper and Strominger suggested long ago that beta-lactams inhibit DD-peptidases because they mimic the D-alanyl-D-alanine motif of the peptidoglycan substrate of these enzymes. They also predicted that beta-lactams having a peptidoglycan-mimetic side-chain might be better antibiotics than their non-specific counterparts, but decades of research have not provided any evidence for this. We have recently described two such novel beta-lactams. The first is a penicillin having the glycyl-L-alpha-amino-epsilon-pimelyl side-chain of Streptomyces strain R61 peptidoglycan, making it the "perfect penicillin" for this organism. The other is a cephalosporin with the same side-chain. Here, we describe the X-ray crystal structures of the perfect penicillin in non-covalent and covalent complexes with the Streptomyces R61 DD-peptidase. The structure of the non-covalent enzyme-inhibitor complex is the first such complex to be trapped crystallographically with a DD-peptidase. In addition, the covalent complex of the peptidyl-cephalosporin with the R61 DD-peptidase is described. Finally, two covalent complexes with the traditional beta-lactams benzylpenicillin and cephalosporin C were determined for comparison with the peptidyl beta-lactams. These structures, together with relevant kinetics data, support Tipper and Strominger's assertion that peptidoglycan-mimetic side-chains should improve beta-lactams as inhibitors of DD-peptidases.


    Related Citations: 
    • Structures of Two Kinetic Intermediates Reveal Species Specificity of Penicillin-Binding Proteins
      Mcdonough, M.A.,Anderson, J.W.,Silvaggi, N.R.,Pratt, R.F.,Knox, J.R.,Kelly, J.A.
      (2002) J.Mol.Biol. 322: 111
    • 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
    • A 1.2-A Snapshot of the Final Step of Bacterial Cell Wall Biosynthesis
      Lee, W.,Mcdonough, M.A.,Kotra, L.,Li, Z.H.,Silvaggi, N.R.,Takeda, Y.,Kelly, J.A.,Mobashery, S.
      (2001) Proc.Natl.Acad.Sci.USA 98: 1427


    Organizational Affiliation

    Department of Molecular and Cell Biology and Institute for Materials Science, University of Connecticut, Storrs, CT 06269-3125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanyl-D-alanine carboxypeptidase precursor
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
0MU
Query on 0MU

Download SDF File 
Download CCD File 
A
(2R)-5-(acetyloxymethyl)-2-[(1R)-1-[[(5R)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexanoyl]amino]-2-oxidanylidene-ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
CEPHALOSPORIN C, bound form
C16 H23 N3 O8 S
KPDUYBJZYVMEKK-ICUOPCATSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.000α = 90.00
b = 67.000β = 90.00
c = 100.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
SHELXL-97refinement
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance