2FFF

Open Form of a Class A Transpeptidase Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of an "open" form of PBP1B from Streptococcus pneumoniae.

Lovering, A.L.De Castro, L.Lim, D.Strynadka, N.C.

(2006) Protein Sci. 15: 1701-1709

  • DOI: 10.1110/ps.062112106

  • PubMed Abstract: 
  • The class A PBP1b from Streptococcus pneumoniae is responsible for glycosyltransferase and transpeptidase (TP) reactions, forming the peptidoglycan of the bacterial cell wall. The enzyme has been produced in a stable, soluble form and undergoes time- ...

    The class A PBP1b from Streptococcus pneumoniae is responsible for glycosyltransferase and transpeptidase (TP) reactions, forming the peptidoglycan of the bacterial cell wall. The enzyme has been produced in a stable, soluble form and undergoes time-dependent proteolysis to leave an intact TP domain. Crystals of this TP domain were obtained, diffracting to 2.2 A resolution, and the structure was solved by using molecular replacement. Analysis of the structure revealed an "open" active site, with important conformational differences to the previously determined "closed" apoenzyme. The active-site nucleophile, Ser460, is in an orientation that allows for acylation by beta-lactams. Consistent with the productive conformation of the conserved active-site catalytic residues, adjacent loops show only minor deviation from those of known acyl-enzyme structures. These findings are discussed in the context of enzyme functionality and the possible conformational sampling of PBP1b between active and inactive states.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
penicillin-binding protein 1B
A
15Streptococcus pneumoniaeMutation(s): 0 
Gene Names: pbp1b
Find proteins for Q4TUQ1 (Streptococcus pneumoniae)
Go to UniProtKB:  Q4TUQ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
penicillin-binding protein 1B
B
453Streptococcus pneumoniaeMutation(s): 0 
Gene Names: pbp1b (pbp1B)
Find proteins for O70038 (Streptococcus pneumoniae)
Go to UniProtKB:  O70038
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.661α = 90.00
b = 78.043β = 113.02
c = 60.315γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance