1SCW

TOWARD BETTER ANTIBIOTICS: CRYSTAL STRUCTURE OF R61 DD-PEPTIDASE INHIBITED BY A NOVEL MONOCYCLIC PHOSPHATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.102 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toward Better Antibiotics: Crystallographic Studies of a Novel Class of DD-Peptidase/beta-Lactamase Inhibitors.

Silvaggi, N.R.Kaur, K.Adediran, S.A.Pratt, R.F.Kelly, J.A.

(2004) Biochemistry 43: 7046-7053

  • DOI: 10.1021/bi049612c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-lactam antibiotics are vital weapons in the treatment of bacterial infections, but their future is under increasing threat from beta-lactamases. These bacterial enzymes hydrolyze and inactivate beta-lactam antibiotics, rendering the host cell re ...

    Beta-lactam antibiotics are vital weapons in the treatment of bacterial infections, but their future is under increasing threat from beta-lactamases. These bacterial enzymes hydrolyze and inactivate beta-lactam antibiotics, rendering the host cell resistant to the bactericidal effects of the drugs. Nevertheless, the bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases), the killing targets of beta-lactams, remain attractive targets for antibiotic compounds. Cyclic acyl phosph(on)ates have been developed and investigated as potential inhibitors of both transpeptidases and beta-lactamases. The X-ray crystal structures of the complexes of the Streptomyces strain R61 DD-peptidase inhibited by a bicyclic [1-hydroxy-4,5-benzo-2,6-dioxaphosphorinanone(3)-1-oxide] and a monocyclic [1-hydroxy-4-phenyl-2,6-dioxaphosphorinanone(3)-1-oxide] acyl phosphate were determined to investigate the mode of action of these novel inhibitors. The structures show, first, that these inhibitors form covalent bonds with the active site serine residue of the enzyme and that the refractory complexes thus formed are phosphoryl-enzyme species rather than acyl enzymes. The complexes are long-lived largely because, after ring opening, the ligands adopt conformations that cannot directly recyclize, the latter a phenomenon previously observed with cyclic acyl phosph(on)ates. While the two inhibitors bind in nearly identical conformations, the phosphoryl-enzyme complex formed from the monocyclic compound is significantly less mobile than that formed from the bicyclic compound. Despite this difference, the complex with the bicyclic compound breaks down to regenerate free enzyme somewhat more slowly than that of the monocyclic. This may be because of steric problems associated with the reorientation of the larger bicyclic ligand required for reactivation. The structures are strikingly different in the orientation of the phosphoryl moiety from those generated using more specific phosph(on)ates. Models of the noncovalent complexes of the monocyclic compound with the R61 DD-peptidase and a structurally very similar class C beta-lactamase suggest reasons why the former enzyme is phosphorylated by this compound, while the latter is acylated. Finally, this paper provides information that will help in the design of additional DD-peptidase inhibitors with the potential to serve as leads in the development of novel antibiotics.


    Related Citations: 
    • 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
    • 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 CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOGUE OF A TETRAHEDRAL TRANSITION STATE
      Silvaggi, N.R.,Anderson, J.W.,Brinsmade, S.R.,Pratt, R.F.,Kelly, J.A.
      (2003) Biochemistry 42: 1199


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanyl-D-alanine carboxypeptidase
A
349Streptomyces sp. (strain R61)Mutation(s): 0 
EC: 3.4.16.4
Find proteins for P15555 (Streptomyces sp. (strain R61))
Go to UniProtKB:  P15555
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CP5
Query on CP5

Download SDF File 
Download CCD File 
A
(2Z)-3-{[OXIDO(OXO)PHOSPHINO]OXY}-2-PHENYLACRYLATE
C9 H6 O5 P
WSMRUPUEYOBWRC-VURMDHGXSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.900α = 90.00
b = 66.700β = 90.00
c = 100.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-22
    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