Home  |  Contact
PROSITE documentation PDOC00485 [for PROSITE entry PS51173]

CBM2 (carbohydrate-binding type-2) domain signature and profile





Description

The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8) [1]. Structurally, cellulases and xylanases generally consist of a catalytic domain and a conserved region of ~100 amino acid residues, the carbohydrate-binding module 2 (CBM2) [2,E1]. It is found either at the N-terminal or at the C-terminal extremity of these enzymes.

CBM2 can be classified in 2 subfamilies according to substrate specificities: CBM2a which binds cellulose and CBM2b which interacts specifically with xylan. CBM2a and CBM2b also display significant differences at the residue level as shown in the following schematic representation:

           +-------------------------------------------------+
           |                                                 |
 CBM2a    xCxxxxWxxGxxNxxxxxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx
                                           ********

           +-------------------------------------------------+
           |                                                 |
 CBM2b    xCxxxxWxxRxxNxxxxxxxxxxxWxxxxxxx--------GxxxxxxxxxxCx
'C': conserved cysteine involved in a disulfide bond.
'*': position of the pattern.
'W': surface-exposed tryptophan

Like other CBM domains CBM2 is a β-sheet domain containing a planar face which interacts with its ligand via a hydrophobic strip of aromatic residues (see <PDB:1EXG>) [3]. In family 2a this hydrophobic surface consists of three tryptophan residues, which are all required for binding soluble and insoluble forms of cellulose [4]. In family 2b only 2 surface-exposed tryptophans are conserved and the first one is oriented differently. It is therefore not well oriented to interact with cellulose but is ideal for binding xylan [5].

Enzymes known to contain such a domain are:

  • Endoglucanase (gene end1) from Butyrivibrio fibrisolvens.
  • Endoglucanases A (gene cenA) and B (cenB) from Cellulomonas fimi.
  • Exoglucanases A (gene cbhA) and B (cbhB) from Cellulomonas fimi.
  • Endoglucanase E-2 (gene celB) from Thermomonospora fusca.
  • Endoglucanase A (gene celA) from Microbispora bispora.
  • Endoglucanases A (gene celA), B (celB) and C (celC) from Pseudomonas fluorescens.
  • Endoglucanase A (gene celA) from Streptomyces lividans.
  • Exocellobiohydrolase (gene cex) from Cellulomonas fimi.
  • Xylanases A (gene xynA) and B (xynB) from Pseudomonas fluorescens.
  • Arabinofuranosidase C (EC 3.2.1.55) (xylanase C) (gene xynC) from Pseudomonas fluorescens.
  • Chitinase 63 (EC 3.2.1.14) from Streptomyces plicatus.
  • Chitinase C from Streptomyces lividans.

To recognize the CBM2a domain we developed a pattern which is located in a conserved region specific to CBM2a. We also developed a profile which covers the whole CBM2 domain and recognizes both CBM2 subfamilies.

Last update:

December 2005 / Text revised; profile added.

-------------------------------------------------------------------------------

Technical section

PROSITE methods (with tools and information) covered by this documentation:

CBM2, PS51173; CBM2 (Carbohydrate-binding type-2) domain profile  (MATRIX)

CBM2_A, PS00561; CBM2a (carbohydrate-binding type-2) domain signature  (PATTERN)


References

1AuthorsGilkes N.R. Henrissat B. Kilburn D.G. Miller R.C. Jr. Warren R.A.J.
TitleDomains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.
SourceMicrobiol. Rev. 55:303-315(1991).
PubMed ID1886523

2AuthorsMeinke A. Gilkes N.R. Kilburn D.G. Miller R.C. Jr. Warren R.A.J.
TitleBacterial cellulose-binding domain-like sequences in eucaryotic polypeptides.
SourceProtein Seq. Data Anal. 4:349-353(1991).
PubMed ID1812490

3AuthorsXu G.Y. Ong E. Gilkes N.R. Kilburn D.G. Muhandiram D.R. Harris-Brandts M. Carver J.P. Kay L.E. Harvey T.S.
TitleSolution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy.
SourceBiochemistry 34:6993-7009(1995).
PubMed ID7766609

4AuthorsNagy T. Simpson P. Williamson M.P. Hazlewood G.P. Gilbert H.J. Orosz L.
TitleAll three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.
SourceFEBS. Lett. 429:312-316(1998).
PubMed ID9662439

5AuthorsSimpson P.J. Bolam D.N. Cooper A. Ciruela A. Hazlewood G.P. Gilbert H.J. Williamson M.P.
TitleA family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
SourceStructure. Fold. Des. 7:853-864(1999).
PubMed ID10425686

6AuthorsSimpson P.J. Xie H. Bolam D.N. Gilbert H.J. Williamson M.P.
TitleThe structural basis for the ligand specificity of family 2 carbohydrate-binding modules.
SourceJ. Biol. Chem. 275:41137-41142(2000).
PubMed ID10973978
DOI10.1074/jbc.M006948200

E1Sourcehttp://www.cazy.org/fam/CBM2.html



PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.

Miscellaneous

View entry in original PROSITE document format
View entry in raw text format (no links)