2C1I

Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1073/pnas.0504339102
  • Primary Citation of Related Structures:  

  • 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 hypersensitivi ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDOGLYCAN GLCNAC DEACETYLASE
A
431Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 1 
Gene Names: pgdA
EC: 3.5.1.104
Find proteins for Q8DP63 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DP63
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.275α = 90.00
b = 79.239β = 90.00
c = 100.377γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Database references, Source and taxonomy, Structure summary