Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA)

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor.

Blair, D.E.Schuttelkopf, A.W.MacRae, J.I.van Aalten, D.M.

(2005) Proc Natl Acad Sci U S A 102: 15429-15434

  • DOI: https://doi.org/10.1073/pnas.0504339102
  • Primary Citation of Related Structures:  
    2C1G, 2C1I

  • PubMed Abstract: 

    Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA) protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. Deletion of the pgda gene has been shown to result in hypersensitivity to lysozyme and reduction of infectivity in a mouse model. SpPgdA is a member of the family 4 carbohydrate esterases, for which little structural information exists, and no catalytic mechanism has yet been defined. Here we describe the native crystal structure and product complexes of SpPgdA biochemical characterization and mutagenesis. The structural data show that SpPgdA is an elongated three-domain protein in the crystal. The structure, in combination with mutagenesis, shows that SpPgdA is a metalloenzyme using a His-His-Asp zinc-binding triad with a nearby aspartic acid and histidine acting as the catalytic base and acid, respectively, somewhat similar to other zinc deacetylases such as LpxC. The enzyme is able to accept GlcNAc(3) as a substrate (K(m) = 3.8 mM, k(cat) = 0.55 s(-1)), with the N-acetyl of the middle sugar being removed by the enzyme. The data described here show that SpPgdA and the other family 4 carbohydrate esterases are metalloenzymes and present a step toward identification of mechanism-based inhibitors for this important class of enzymes.

  • Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, DD1 5EH Dundee, Scotland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDOGLYCAN GLCNAC DEACETYLASE431Streptococcus pneumoniae R6Mutation(s): 0 
Find proteins for Q8DP63 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DP63 
Go to UniProtKB:  Q8DP63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DP63
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.529α = 90
b = 78.439β = 90
c = 99.515γ = 90
Software Package:
Software NamePurpose
HKLdata reduction
HKLdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Advisory, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Other