1YHT

Crystal structure analysis of Dispersin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis of Dispersin B, a Biofilm-releasing Glycoside Hydrolase from the Periodontopathogen Actinobacillus actinomycetemcomitans.

Ramasubbu, N.Thomas, L.M.Ragunath, C.Kaplan, J.B.

(2005) J.Mol.Biol. 349: 475-486

  • DOI: 10.1016/j.jmb.2005.03.082

  • PubMed Abstract: 
  • Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix that holds the bacteria together in a mass and firmly attaches the bacterial mass to the underlying surface. A major component of the extracellular polysacch ...

    Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix that holds the bacteria together in a mass and firmly attaches the bacterial mass to the underlying surface. A major component of the extracellular polysaccharide matrix in several phylogenetically diverse bacteria is PGA, a linear polymer of N-acetylglucosamine residues in beta(1,6)-linkage. PGA is produced by the Gram-negative periodontopathogen Actinobacillus actinomycetemcomitans as well as by the Gram-positive device-associated pathogen Staphylococcus epidermidis. We recently reported that A.actinomycetemcomitans produces a soluble glycoside hydrolase named dispersin B, which degrades PGA. Here, we present the crystal structure of dispersin B at 2.0A in complex with a glycerol and an acetate ion at the active site. The enzyme crystallizes in the orthorhombic space group C222(1) with cell dimensions a=41.02A, b=86.13A, c=185.77A. The core of the enzyme consists a (beta/alpha)(8) barrel topology similar to other beta-hexosaminidases but significant differences exist in the arrangement of loops hovering in the vicinity of the active site. The location and interactions of the glycerol and acetate moieties in conjunction with the sequence analysis suggest that dispersin B cleaves beta(1,6)-linked N-acetylglucosamine polymer using a catalytic machinery similar to other family 20 hexosaminidases which cleave beta(1,4)-linked N-acetylglucosamine residues.


    Related Citations: 
    • Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity
      Kaplan, J.B.,Ragunath, C.,Ramasubbu, N.,Fine, D.H.
      (2003) J.Bacteriol. 185: 4693
    • Genes involved in the synthesis and degradation of matrix polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae biofilms.
      Kaplan, J.B.,Velliyagounder, K.,Ragunath, C.,Rhode, H.,Mack, D.,Knobloch, J.K.,Ramasubbu, N.
      (2004) J.Bacteriol. 186: 8213
    • Enzymatic detachment of Staphylococcus epidermidis biofilms
      Kaplan, J.B.,Ragunath, C.,Velliyagounder, K.,Fine, D.H.,Ramasubbu, N.
      (2004) Antimicrob.Agents Chemother. --: 2633


    Organizational Affiliation

    Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA. ramasun1@umdnj.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DspB
A
367Aggregatibacter actinomycetemcomitansGene Names: dspB
Find proteins for Q840G9 (Aggregatibacter actinomycetemcomitans)
Go to UniProtKB:  Q840G9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.151 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 41.023α = 90.00
b = 86.129β = 90.00
c = 185.774γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance