2J1E

High Resolution Crystal Structure of CBM32 from a N-acetyl-beta- hexosaminidase in complex with lacNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report



Literature

The Interaction of a Carbohydrate-Binding Module from a Clostridium Perfringens N-Acetyl-Beta-Hexosaminidase with its Carbohydrate Receptor

Ficko-Blean, E.Boraston, A.B.

(2006) J Biol Chem 281: 37748

  • DOI: 10.1074/jbc.M606126200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Clostridium perfringens is a notable colonizer of the human gastrointestinal tract. This bacterium is quite remarkable for a human pathogen by the number of glycoside hydrolases found in its genome. The modularity of these enzymes is striking as is t ...

    Clostridium perfringens is a notable colonizer of the human gastrointestinal tract. This bacterium is quite remarkable for a human pathogen by the number of glycoside hydrolases found in its genome. The modularity of these enzymes is striking as is the frequent occurrence of modules having amino acid sequence identity with family 32 carbohydrate-binding modules (CBMs), often referred to as F5/8 domains. Here we report the properties of family 32 CBMs from a C. perfringens N-acetyl-beta-hexosaminidase. Macroarray, UV difference, and isothermal titration calorimetry binding studies indicate a preference for the disaccharide LacNAc (beta-d-galactosyl-1,4-beta-d-N-acetylglucosamine). The molecular details of the interaction of this CBM with galactose, LacNAc, and the type II blood group H-trisaccharide are revealed by x-ray crystallographic studies at resolutions of 1.49, 2.4, and 2.3 A, respectively.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYALURONIDASEA150Clostridium perfringens ATCC 13124Mutation(s): 0 
Gene Names: nagJCPF_1442
EC: 3.2.1.169
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
B
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.377α = 90
b = 77.377β = 90
c = 73.421γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary