2YA1

Product complex of a multi-modular glycogen-degrading pneumococcal virulence factor SpuA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Conformation and Function of a Multimodular Glycogen-Degrading Pneumococcal Virulence Factor.

Lammerts Van Bueren, A.Ficko-Blean, E.Pluvinage, B.Hehemann, J.Higgins, M.A.Deng, L.Ogunniyi, A.D.Stroeher, U.H.El Warry, N.Burke, R.D.Czjzek, M.Paton, J.C.Vocadlo, D.J.Boraston, A.B.

(2011) Structure 19: 640

  • DOI: 10.1016/j.str.2011.03.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SpuA is a large multimodular cell wall-attached enzyme involved in the degradation of glycogen by the pathogenic bacterium Streptococcus pneumoniae. The deletion of the gene encoding SpuA from the bacterium resulted in a strain with reduced competiti ...

    SpuA is a large multimodular cell wall-attached enzyme involved in the degradation of glycogen by the pathogenic bacterium Streptococcus pneumoniae. The deletion of the gene encoding SpuA from the bacterium resulted in a strain with reduced competitiveness in a mouse model of virulence relative to the parent strain, linking the degradation of host-glycogen to the virulence of the bacterium. Through the combined use of X-ray crystallography, small-angle X-ray scattering, and inhibitor binding, the molecular features involved in substrate recognition by this complex protein are revealed. This uniquely illustrates the complexity of the active site, the conformational changes incurred during carbohydrate binding by this protein, and the interaction and cooperation of its composite modules during this process. New insight into the function of this particular pneumococcal virulence factor is provided along with substantial contributions to the nascent framework for understanding the structural and functional interplay between modules in multimodular carbohydrate-active enzymes.


    Organizational Affiliation

    Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE ALKALINE AMYLOPULLULANASE
A
1014Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
Find proteins for A0A0H2UNG0 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2UNG0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.137α = 90.00
b = 86.429β = 90.00
c = 193.225γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Data collection