2J7M | pdb_00002j7m

Characterization of a Family 32 CBM

• PDB DOI: https://doi.org/10.2210/pdb2J7M/pdb
• Entry: 2J7M supersedes: 2J1F

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-12 Released: 2006-10-16 
• Deposition Author(s): Ficko-Blean, E., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.251 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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 Biological Chem 281: 37748

• PubMed: 16990278 
• DOI: https://doi.org/10.1074/jbc.M606126200
• Primary Citation Related Structures: 
  2J1A, 2J1E, 2J7M


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.86 kDa 
• Atom Count: 1,349 
• Modeled Residue Count: 143 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYALURONIDASE	A	149	Clostridium perfringens	Mutation(s): 0  EC: 3.2.1.169
UniProt
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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G42956UG GlyCosmos: G42956UG GlyGen: G42956UG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900125	B	H type 2 antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.251 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.315	α = 90
b = 77.315	β = 90
c = 74.162	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-16 
Deposition Author(s): Ficko-Blean, E., Boraston, A.B.
• This entry supersedes: 2J1F

Revision History  

• Version 1.0: 2006-10-16
  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
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Structure summary