1W79

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Actinomadura R39 Dd-Peptidase Reveals New Domains in Penicillin-Binding Proteins.

Sauvage, E.Herman, R.Petrella, S.Duez, C.Bouillenne, F.Frere, J.M.Charlier, P.

(2005) J.Biol.Chem. 280: 31249

  • DOI: 10.1074/jbc.M503271200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high beta-lactam-binding activity (second order rate constant for ...

    Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high beta-lactam-binding activity (second order rate constant for the acylation of the active site serine by benzylpenicillin: k2/K = 300 mm(-1) s(-1)). The crystal structure of the DD-peptidase from Actinomadura R39 was solved at a resolution of 1.8 angstroms by single anomalous dispersion at the cobalt resonance wavelength. The structure is composed of three domains: a penicillin-binding domain similar to the penicillin-binding domain of E. coli PBP5 and two domains of unknown function. In most multimodular PBPs, additional domains are generally located at the C or N termini of the penicillin-binding domain. In R39, the other two domains are inserted in the penicillin-binding domain, between the SXXK and SXN motifs, in a manner similar to "Matryoshka dolls." One of these domains is composed of a five-stranded beta-sheet with two helices on one side, and the other domain is a double three-stranded beta-sheet inserted in the previous domain. Additionally, the 2.4-angstroms structure of the acyl-enzyme complex of R39 with nitrocefin reveals the absence of active site conformational change upon binding the beta-lactams.


    Related Citations: 
    • Primary and Predicted Secondary Structure of the Actinomadura R39 Extracellular Dd-Peptidase, a Penicillin-Binding Protein (Pbp) Related to the Escherichia Coli Pbp4
      Granier, B.,Duez, C.,Lepage, S.,Englbert, S.,Dusart, J.,Dideberg, O.,Van Beeumen, J.,Frere, J.M.,Ghuysen, J.M.
      (1992) Biochem J. 286: 981


    Organizational Affiliation

    Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5, B-4000 Liège, Belgium. eric.sauvage@ulg.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
A, B, C, D
489Actinomadura sp. (strain R39)Mutation(s): 0 
Gene Names: dac
EC: 3.4.16.4
Find proteins for P39045 (Actinomadura sp. (strain R39))
Go to UniProtKB:  P39045
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 105.187α = 90.00
b = 93.369β = 94.25
c = 107.272γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SOLVEphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance