2VNG

Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by Clostridium perfringens in complex with blood group A-trisaccharide ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Divergent Modes of Glycan Recognition by a New Family of Carbohydrate-Binding Modules

Gregg, K.J.Finn, R.Abbott, D.W.Boraston, A.B.

(2008) J.Biol.Chem. 283: 12604

  • DOI: 10.1074/jbc.M709865200
  • Primary Citation of Related Structures:  2VMG, 2VMH, 2VMI, 2VNO, 2VNR

  • PubMed Abstract: 
  • The genomes of myonecrotic Clostridium perfringens isolates contain genes encoding a large and fascinating array of highly modular glycoside hydrolase enzymes. Although the catalytic activities of many of these enzymes are somewhat predictable based ...

    The genomes of myonecrotic Clostridium perfringens isolates contain genes encoding a large and fascinating array of highly modular glycoside hydrolase enzymes. Although the catalytic activities of many of these enzymes are somewhat predictable based on their amino acid sequences, the functions of their abundant ancillary modules are not and remain poorly studied. Here, we present the structural and functional analysis of a new family of ancillary carbohydrate-binding modules (CBMs), CBM51, which was previously annotated in data bases as the novel putative CBM domain. The high resolution crystal structures of two CBM51 members, GH95CBM51 and GH98CBM51, from a putative family 95 alpha-fucosidase and from a family 98 blood group A/B antigen-specific endo-beta-galactosidase, respectively, showed them to have highly similar beta-sandwich folds. However, GH95CBM51 was shown by glycan microarray screening, isothermal titration calorimetry, and x-ray crystallography to bind galactose residues, whereas the same analyses of GH98CBM51 revealed specificity for the blood group A/B antigens through non-conserved interactions. Overall, this work identifies a new family of CBMs with many members having apparent specificity for eukaryotic glycans, in keeping with the glycan-rich environment C. perfringens would experience in its host. However, a wider bioinformatic analysis of this CBM family also indicated a large number of members in non-pathogenic environmental bacteria, suggesting a role in the recognition of environmental glycans.


    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
CPE0329
A, B
180Clostridium perfringens (strain 13 / Type A)N/A
Find proteins for Q8XNK4 (Clostridium perfringens (strain 13 / Type A))
Go to UniProtKB:  Q8XNK4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
A, B
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.683α = 90.00
b = 98.754β = 90.00
c = 49.241γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection