Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

Morlot, C.Pernot, L.Le Gouellec, A.Di Guilmi, A.M.Vernet, T.Dideberg, O.Dessen, A.

(2005) J Biol Chem 280: 15984-15991

  • DOI: https://doi.org/10.1074/jbc.M408446200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Penicillin-binding proteins (PBPs) are membrane-associated enzymes which perform critical functions in the bacterial cell division process. The single d-Ala,d-Ala (d,d)-carboxypeptidase in Streptococcus pneumoniae, PBP3, has been shown to play a key role in control of availability of the peptidoglycal substrate during cell growth. Here, we have biochemically characterized and solved the crystal structure of a soluble form of PBP3 to 2.8 A resolution. PBP3 folds into an NH(2)-terminal, d,d-carboxypeptidase-like domain, and a COOH-terminal, elongated beta-rich region. The carboxypeptidase domain harbors the classic signature of the penicilloyl serine transferase superfamily, in that it contains a central, five-stranded antiparallel beta-sheet surrounded by alpha-helices. As in other carboxypeptidases, which are present in species whose peptidoglycan stem peptide has a lysine residue at the third position, PBP3 has a 14-residue insertion at the level of its omega loop, a feature that distinguishes it from carboxypeptidases from bacteria whose peptidoglycan harbors a diaminopimelate moiety at this position. PBP3 performs substrate acylation in a highly efficient manner (k(cat)/K(m) = 50,500 M(-1) x s(-1)), an event that may be linked to role in control of pneumococcal peptidoglycan reticulation. A model that places PBP3 poised vertically on the bacterial membrane suggests that its COOH-terminal region could act as a pedestal, placing the active site in proximity to the peptidoglycan and allowing the protein to "skid" on the surface of the membrane, trimming pentapeptides during the cell growth and division processes.

  • Organizational Affiliation

    Laboratoire de Cristallographie Macromoléculaire and Laboratoire d'Ingénierie des Macromolécules, Institut de Biologie Structurale Jean-Pierre Ebel (CNRS/CEA/UJF), 41 rue Jules Horowitz, Grenoble 38027, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl-D-alanine carboxypeptidase
A, B, C, D
379Streptococcus pneumoniae R6Mutation(s): 9 
Gene Names: dacA
Find proteins for Q8DQ99 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQ99 
Go to UniProtKB:  Q8DQ99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQ99
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
O4 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.608α = 90
b = 120.839β = 90
c = 177.076γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection