PROSITE documentation PDOC51172

CBM3 (carbohydrate binding type-3) domain profile




Description

Carbohydrate-binding modules (CBM) have been classified into more than 40 families according to sequence homology [E1]. Several cellulolytic enzymes share a conserved region of about 150 amino acid residues, the CBM3 domain [1]. It has been classified in three different subtypes, termed family IIIa, IIIb and IIIc. The family IIIa (scaffoldin) and IIIb (mainly free enzymes) are closely similar in their primary structures and both types bind strongly to crystalline cellulose [2,3]. Members of the family IIIc, fails to bind crystalline cellulose, but serves in a 'helper' capacity by feeding a single incoming cellulose chain into the active site of the neighbouring catalytic module pending hydrolysis [4,5].

The CBM3 domain is mainly found C-terminal to the catalytic domain, which correspond to a wide range of bacterial glycosyl hydrolases like family 9 (see <PDOC00511>), family 5 (see <PDOC00565>) and family 10 (see <PDOC00510>).

The crystal structure of CBM3 has been solved (see <PDB:1NBC>) [2]. It consists of nine β-strands which form a compact domain that has an overall prismatic shape. It is arranged in two antiparallel β-sheets that stack face-to-face to form a β sandwich with jelly roll topology. Two defined surfaces, located on opposite sides of the molecule, contain conserved polar and aromatic residues which are probably involved in the binding of the CBM to cellulose [2,3]. The first one forms a planar strip whereas the second one forms a shallow groove.

Some proteins known to contain a CBM3 domain are listed below:

  • Clostridial cellulosomal scaffolding proteins cipA, cipC and cbpA. They promote the binding of cellulose to the catalytic domains of the cellulolytic enzymes.
  • Bacterial cellulases A, B, F, G, I, N, Y, Z (Endo-1,4-β-glucanase) (EC 3.2.1.4).

The profile we developed covers the whole CBM3 domain.

Note:

The CBM3 domain is also known as cellulose-binding domain family III (CBD III).

Last update:

December 2005 / First entry.

Technical section

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

CBM3, PS51172; CBM3 (carbohydrate binding type-3) domain profile  (MATRIX)


References

1AuthorsPoole D.M., Morag E., Lamed R., Bayer E.A., Hazlewood G.P., Gilbert H.J.
TitleIdentification of the cellulose-binding domain of the cellulosome subunit S1 from Clostridium thermocellum YS.
SourceFEMS Microbiol. Lett. 78:181-186(1992).
PubMed ID1490597

2AuthorsTormo J., Lamed R., Chirino A.J., Morag E., Bayer E.A., Shoham Y., Steitz T.A.
TitleCrystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose.
SourceEMBO J. 15:5739-5751(1996).
PubMed ID8918451

3AuthorsShimon L.J.W., Pages S., Belaich A., Belaich J.-P., Bayer E.A., Lamed R., Shoham Y., Frolow F.
TitleStructure of a family IIIa scaffoldin CBD from the cellulosome of Clostridium cellulolyticum at 2.2 A resolution.
SourceActa Crystallogr. D 56:1560-1568(2000).
PubMed ID11092922

4AuthorsIrwin D., Shin D.-H., Zhang S., Barr B.K., Sakon J., Karplus P.A., Wilson D.B.
TitleRoles of the catalytic domain and two cellulose binding domains of Thermomonospora fusca E4 in cellulose hydrolysis.
SourceJ. Bacteriol. 180:1709-1714(1998).
PubMed ID9537366

5AuthorsGal L., Pages S., Gaudin C., Belaich A., Reverbel-Leroy C., Tardif C., Belaich J.-P.
TitleCharacterization of the cellulolytic complex (cellulosome) produced by Clostridium cellulolyticum.
SourceAppl. Environ. Microbiol. 63:903-909(1997).
PubMed ID9055408

E1Sourcehttp://www.cazy.org/fam/CBM3.html



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