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PDBsum entry 1yht
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Hydrolase PDB id
1yht

 

 

 

 

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Contents
Protein chain
344 a.a. *
Ligands
ACY
GOL ×2
Waters ×243
* Residue conservation analysis
PDB id:
1yht
Name: Hydrolase
Title: Crystal structure analysis of dispersin b
Structure: Dspb. Chain: a. Engineered: yes
Source: Aggregatibacter actinomycetemcomitans. Organism_taxid: 714. Strain: cu1000. Gene: dspb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.154     R-free:   0.211
Authors: N.Ramasubbu,L.M.Thomas,C.Ragunath,J.B.Kaplan
Key ref:
N.Ramasubbu et al. (2005). Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans. J Mol Biol, 349, 475-486. PubMed id: 15878175 DOI: 10.1016/j.jmb.2005.03.082
Date:
10-Jan-05     Release date:   10-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q840G9  (Q840G9_AGGAC) -  DspB (Fragment) from Aggregatibacter actinomycetemcomitans
Seq:
Struc: 		361 a.a.
344 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.52  - beta-N-acetylhexosaminidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

 

 
DOI no: 10.1016/j.jmb.2005.03.082 J Mol Biol 349:475-486 (2005)
PubMed id: 15878175  
 
 
Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans.
N.Ramasubbu, L.M.Thomas, C.Ragunath, J.B.Kaplan.
 
  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 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The topology and comparison with the homologues of DspB. (a) Schematic topogram generated by the program TOPS located at the URL (http://www.tops.leeds.ac.uk/). a-Helices are represented by cylinders and b-strands by arrows. (b) Ribbon diagram for the refined structure of DspB showing the TIM barrel down the barrel axis. (c) A 2F[o] -F[c] difference density map around the putative active site. The map is contoured at 1.5s. The refined model of DspB has been superimposed. (d) Superposition of 1HP5 (green) and DspB (magenta) by least-squares fit as derived from the program SPDBV (http://www.expasy.org/spdbv/). 		Figure 4.
Figure 4. Diagrammatic illustration of the interactions formed by the ligands bound in the active sites of DspB (a) and 1HP5 (b). The hydrogen bond interactions are indicated with a broken line. An arc with radiating lines represents the hydrophobic interactions in the structure. The glycerol is labeled as Gol. (c) Superposition of active site residues at subsite -1 of 1HP5 (magenta) with the corresponding residue from DspB (green). Note that the residues in both the enzymes are almost conserved. Note also the absence of the Trp408 residue in DspB and the difference in the loop conformation and length in DspB.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 349, 475-486) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21214870 A.Dashiff, and D.E.Kadouri (2011).
Predation of oral pathogens by Bdellovibrio bacteriovorus 109J.
  Mol Oral Microbiol, 26, 19-34.  
21290547 Y.Yang, T.Liu, Y.Yang, Q.Wu, Q.Yang, and B.Yu (2011).
Synthesis, Evaluation, and Mechanism of N,N,N-Trimethyl-D-glucosamine-(1→4)-chitooligosaccharides as Selective Inhibitors of Glycosyl Hydrolase Family 20 β-N-Acetyl-D-hexosaminidases.
  Chembiochem, 12, 457-467.  
19633088 A.H.Choi, L.Slamti, F.Y.Avci, G.B.Pier, and T.Maira-Litrán (2009).
The pgaABCD locus of Acinetobacter baumannii encodes the production of poly-beta-1-6-N-acetylglucosamine, which is critical for biofilm formation.
  J Bacteriol, 191, 5953-5963.  
19561191 J.Wu, and C.Xi (2009).
Evaluation of different methods for extracting extracellular DNA from the biofilm matrix.
  Appl Environ Microbiol, 75, 5390-5395.  
18951906 C.Ragunath, S.G.Manuel, V.Venkataraman, H.B.Sait, C.Kasinathan, and N.Ramasubbu (2008).
Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding.
  J Mol Biol, 384, 1232-1248.  
19133500 J.E.Kerrigan, C.Ragunath, L.Kandra, G.Gyémánt, A.Lipták, L.Jánossy, J.B.Kaplan, and N.Ramasubbu (2008).
Modeling and biochemical analysis of the activity of antibiofilm agent Dispersin B.
  Acta Biol Hung, 59, 439-451.  
18204904 J.H.Lee, J.B.Kaplan, and W.Y.Lee (2008).
Microfluidic devices for studying growth and detachment of Staphylococcus epidermidis biofilms.
  Biomed Microdevices, 10, 489-498.  
17548491 G.Donelli, I.Francolini, D.Romoli, E.Guaglianone, A.Piozzi, C.Ragunath, and J.B.Kaplan (2007).
Synergistic activity of dispersin B and cefamandole nafate in inhibition of staphylococcal biofilm growth on polyurethanes.
  Antimicrob Agents Chemother, 51, 2733-2740.  
17114249 G.Parise, M.Mishra, Y.Itoh, T.Romeo, and R.Deora (2007).
Role of a putative polysaccharide locus in Bordetella biofilm development.
  J Bacteriol, 189, 750-760.  
17949435 S.G.Manuel, C.Ragunath, H.B.Sait, E.A.Izano, J.B.Kaplan, and N.Ramasubbu (2007).
Role of active-site residues of dispersin B, a biofilm-releasing beta-hexosaminidase from a periodontal pathogen, in substrate hydrolysis.
  FEBS J, 274, 5987-5999.  
16930309 D.H.Fine, J.B.Kaplan, S.C.Kachlany, and H.C.Schreiner (2006).
How we got attached to Actinobacillus actinomycetemcomitans: A model for infectious diseases.
  Periodontol 2000, 42, 114-157.  
16930303 M.E.Davey, and J.W.Costerton (2006).
Molecular genetics analyses of biofilm formation in oral isolates.
  Periodontol 2000, 42, 13-26.  
16930306 P.E.Kolenbrander, R.J.Palmer, A.H.Rickard, N.S.Jakubovics, N.I.Chalmers, and P.I.Diaz (2006).
Bacterial interactions and successions during plaque development.
  Periodontol 2000, 42, 47-79.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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