CBM_3

Cellulose binding domain

• SMART accession number: SM01067
• Description: -
• Interpro abstract (IPR001956):

  Carbohydrate-binding modules (CBM) have been classified into more than 40 families according to sequence homology. Several cellulolytic enzymes share a conserved region of about 150 amino acid residues, the CBM3 domain [ (PUBMED:1490597) ]. 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 [ (PUBMED:8918451) (PUBMED:11092922) ]. Members of the family IIIc, fail to bind crystalline cellulose, but serve in a 'helper' capacity by feeding a single incoming cellulose chain into the active site of the neighbouring catalytic module pending hydrolysis [ (PUBMED:9537366) (PUBMED:9055408) ].

  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, family 5 and family 10.

  The crystal structure of CBM3 has been solved [ (PUBMED:8918451) ]. It consists of nine beta-strands which form a compact domain that has an overall prismatic shape. It is arranged in two antiparallel beta-sheets that stack face-to-face to form a beta 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 [ (PUBMED:8918451) (PUBMED:11092922) ]. 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-beta-glucanase, EC 3.2.1.4 ).

  This entry represents the CBM3 domain, which is also known as cellulose-binding domain family III (CBD III).

• GO process: carbohydrate metabolic process (GO:0005975)
• GO function: cellulose binding (GO:0030248)

There are 2662 CBM_3 domains in 2304 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Cellular role: metabolism
Binding / catalysis: Cellulose binding

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Tormo J et al.
• Crystal structure of a bacterial family-III cellulose-binding domain: ageneral mechanism for attachment to cellulose.
• EMBO J. 1996; 15: 5739-51

The crystal structure of a family-III cellulose-binding domain (CBD) fromthe cellulosomal scaffoldin subunit of Clostridium thermocellum has beendetermined at 1.75 A resolution. The protein forms a nine-stranded betasandwich with a jelly roll topology and binds a calcium ion. conserved,surface-exposed residues map into two defined surfaces located on oppositesides of the molecule. One of these faces is dominated by a planar linearstrip of aromatic and polar residues which are proposed to interact withcrystalline cellulose. The other conserved residues are contained in ashallow groove, the function of which is currently unknown, and which hasnot been observed previously in other families of CBDs. On the basis ofmodeling studies combined with comparisons of recently determined NMRstructures for other CBDs, a general model for the binding of CBDs tocellulose is presented. Although the proposed binding of the CBD tocellulose is essentially a surface interaction, specific types andcombinations of amino acids appear to interact selectively with glucosemoieties positioned on three adjacent chains of the cellulose surface. Themajor interaction is characterized by the planar strip of aromaticresidues, which align along one of the chains. In addition, polar aminoacid residues are proposed to anchor the CBD molecule to two otheradjacent chains of crystalline cellulose.

• Poole DM, Morag E, Lamed R, Bayer EA, Hazlewood GP, Gilbert HJ
• Identification of the cellulose-binding domain of the cellulosome subunitS1 from Clostridium thermocellum YS.
• FEMS Microbiol Lett. 1992; 78: 181-6

The 3' region of a gene designated cipB, which shows strong homology withcipA that encodes the cellulosome SL subunit of Clostridium thermocellumATCC 27405, was isolated from a gene library of C. thermocellum strain YS.The truncated S1 protein encoded by the cipB derivative bound tightly tocellulose. The cellulose-binding domain in this polypeptide consisted of aC-terminal proximal 167 residue sequence which showed complete identitywith residues 337-503 of mature SL from C. thermocellum strain ATCC 27405.The cellulose-binding domain interacted with both crystalline andamorphous cellulose, but not with xylan.

Structure (3D structures containing this domain)

3D Structures of CBM_3 domains in PDB

PDB code	Title
1g43	CRYSTAL STRUCTURE OF A FAMILY IIIA CBD FROM CLOSTRIDIUM CELLULOLYTICUM
1g87	THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLULOLYTICUM
1ga2	THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLULOLYTICUM COMPLEXED WITH CELLOBIOSE
1js4	ENDO/EXOCELLULASE:CELLOBIOSE FROM THERMOMONOSPORA
1k72	The X-ray Crystal Structure Of Cel9G Complexed With cellotriose
1kfg	The X-ray Crystal Structure of Cel9G from Clostridium cellulolyticum complexed with a Thio-Oligosaccharide Inhibitor
1nbc	BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN
1tf4	ENDO/EXOCELLULASE FROM THERMOMONOSPORA
2l8a	Structure of a novel CBM3 lacking the calcium-binding site
2wnx	3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum
2wo4	3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum, in-house data
2wob	3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum. Orthorhombic structure
2xbt	Structure of a scaffoldin carbohydrate-binding module family 3b from the cellulosome of Bacteroides cellulosolvens: Structural diversity and implications for carbohydrate binding
2xfg	Reassembly and co-crystallization of a family 9 processive endoglucanase from separately expressed GH9 and CBM3c modules
2ylk	Carbohydrate-binding module CBM3b from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum
3tf4	ENDO/EXOCELLULASE:CELLOTRIOSE FROM THERMOMONOSPORA
3zqw	Structure of CBM3b of major scaffoldin subunit ScaA from Acetivibrio cellulolyticus
3zqx	Carbohydrate-binding module CBM3b from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum
3zu8	STRUCTURE OF CBM3B OF MAJOR SCAFFOLDIN SUBUNIT SCAA FROM ACETIVIBRIO CELLULOLYTICUS DETERMINED ON THE NIKEL ABSORPTION EDGE
3zuc	Structure of CBM3b of major scaffoldin subunit ScaA from Acetivibrio cellulolyticus determined from the crystals grown in the presence of Nickel
4b96	Family 3b carbohydrate-binding module from the biomass sensoring system of Clostridium clariflavum
4b97	Biomass sensing modules from putative Rsgi-like proteins of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome
4b9c	Biomass sensoring modules from putative Rsgi-like proteins of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome
4b9f	High resolution structure for family 3a carbohydrate binding module from the cipA scaffolding of clostridium thermocellum
4b9p	Biomass sensoring module from putative Rsgi2 protein of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome
4c8x	Crystal structure of carbohydrate-binding module CBM3b mutant (Y56S) from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum
4jo5	CBM3a-L domain with flanking linkers from scaffoldin cipA of cellulosome of Clostridium thermocellum
4tf4	ENDO/EXOCELLULASE:CELLOPENTAOSE FROM THERMOMONOSPORA

Links (links to other resources describing this domain)

• INTERPRO: IPR001956
• PFAM: CBM_3