2XQX

Structure of the family 32 carbohydrate-binding module from Streptococcus pneumoniae EndoD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Analysis of a Putative Family 32 Carbohydrate-Binding Module from the Streptococcus Pneumoniae Enzyme Endod.

Abbott, D.W.Boraston, A.B.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 429

  • DOI: 10.1107/S1744309111001874
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • EndoD is an architecturally complex endo-β-1,4-N-acetylglucosamidase from Streptococcus pneumoniae that cleaves the chitobiose core of N-linked glycans and contributes to pneumococcal virulence. Although the glycoside hydrolase family 85 catalytic mo ...

    EndoD is an architecturally complex endo-β-1,4-N-acetylglucosamidase from Streptococcus pneumoniae that cleaves the chitobiose core of N-linked glycans and contributes to pneumococcal virulence. Although the glycoside hydrolase family 85 catalytic module has been structurally and functionally characterized, nothing is known about the ancillary modules and how they contribute to the overall function of the enzyme. Presented here is the 2.0 Å resolution structure of a family 32 carbohydrate-binding module of EndoD, SpCBM32, solved by single-wavelength anomalous dispersion. The putative binding site of this protein is a charge-neutral relatively flat region on the protein surface that contains one prominently exposed tryptophan residue that extends into the solvent. These topographical features are discussed in the biological context of EndoD activity and a hypothesis is made about the complex structure of its potential carbohydrate ligand.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC V8W 3P6, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-BETA-N-ACETYLGLUCOSAMINIDASE DA, B151Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: SP_0498
Find proteins for A0A0H2UNT5 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UNT5 
Go to UniProtKB:  A0A0H2UNT5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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: 2.01 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.105α = 90
b = 73.51β = 96.52
c = 34.597γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references, Version format compliance