3ECQ

Endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae: SeMet structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design.

Caines, M.E.Zhu, H.Vuckovic, M.Willis, L.M.Withers, S.G.Wakarchuk, W.W.Strynadka, N.C.

(2008) J Biol Chem 283: 31279-31283

  • DOI: 10.1074/jbc.C800150200
  • Primary Citation of Related Structures:  
    3ECQ

  • PubMed Abstract: 
  • Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase is a cell surface-anchored glycoside hydrolase from family GH101 involved in the breakdown of mucin type O-linked glycans. The 189-kDa mature enzyme specifically hydrolyzes the T-antigen disaccharide from extracellular host glycoproteins and is representative of a broadly important class of virulence factors that have remained structurally uncharacterized due to their large size and highly modular nature ...

    Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase is a cell surface-anchored glycoside hydrolase from family GH101 involved in the breakdown of mucin type O-linked glycans. The 189-kDa mature enzyme specifically hydrolyzes the T-antigen disaccharide from extracellular host glycoproteins and is representative of a broadly important class of virulence factors that have remained structurally uncharacterized due to their large size and highly modular nature. Here we report a 2.9 angstroms resolution crystal structure that remarkably captures the multidomain architecture and characterizes a catalytic center unexpectedly resembling that of alpha-amylases. Our analysis presents a complete model of glycoprotein recognition and provides a basis for the structure-based design of novel Streptococcus vaccines and therapeutics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Centre for Blood Research and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-alpha-N-acetylgalactosaminidaseA, B1531Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: spr0328
EC: 3.2.1.97
Find proteins for Q8DR60 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DR60 
Go to UniProtKB:  Q8DR60
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.611α = 90
b = 158.209β = 90
c = 112.436γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance