Carbohydrate-binding module

In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes (for example glycoside hydrolases). The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains.^[1] CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently (June 2011) 64 families of CBM in the CAZy database.^[2]

CBM_1
three-dimensional structures of three engineered cellulose-binding domains of cellobiohydrolase i from trichoderma reesei, nmr, 18 structures
Identifiers
Symbol	CBM_1
Pfam	PF00734
InterPro	IPR000254
PROSITE	PDOC00486
SCOP2	1cel / SCOPe / SUPFAM
CAZy	CBM1
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_2
solution structure of a cellulose binding domain from cellulomonas fimi by nuclear magnetic resonance spectroscopy
Identifiers
Symbol	CBM_2
Pfam	PF00553
Pfam clan	CL0203
InterPro	IPR001919
PROSITE	PDOC00485
SCOP2	1exg / SCOPe / SUPFAM
CAZy	CBM2
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_3
crystal structure of a family iiia cbd from clostridium cellulolyticum
Identifiers
Symbol	CBM_3
Pfam	PF00942
Pfam clan	CL0203
InterPro	IPR001956
SCOP2	1nbc / SCOPe / SUPFAM
CAZy	CBM3
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_5/12
interactions of a family 18 chitinase with the designed inhibitor hm508, and its degradation product, chitobiono-delta-lactone
Identifiers
Symbol	CBM_5_12
Pfam	PF02839
InterPro	IPR003610
SCOP2	1ed7 / SCOPe / SUPFAM
CAZy	CBM12
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_6
cbm6ct from clostridium thermocellum in complex with xylopentaose
Identifiers
Symbol	CBM_6
Pfam	PF03422
Pfam clan	CL0202
InterPro	IPR005084
SCOP2	1gmm / SCOPe / SUPFAM
CAZy	CBM6
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_4/9
cbm4 structure and function
Identifiers
Symbol	CBM_4_9
Pfam	PF02018
Pfam clan	CL0202
InterPro	IPR003305
SCOP2	1ulp / SCOPe / SUPFAM
CAZy	CBM22
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_10
solution structure of type x cbm
Identifiers
Symbol	CBM_10
Pfam	PF02013
InterPro	IPR002883
SCOP2	1qld / SCOPe / SUPFAM
CAZy	CBM10
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_11
family 11 carbohydrate-binding module of cellulosomal cellulase lic26a-cel5e of clostridium thermocellum
Identifiers
Symbol	CBM_11
Pfam	PF03425
Pfam clan	CL0202
InterPro	IPR005087
CAZy	CBM11
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_14
Identifiers
Symbol	CBM_14
Pfam	PF01607
Pfam clan	CL0155
InterPro	IPR002557
SCOP2	1dqc / SCOPe / SUPFAM
CAZy	CBM14
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_15
xylan-binding module cbm15
Identifiers
Symbol	CBM_15
Pfam	PF03426
Pfam clan	CL0202
InterPro	IPR005088
SCOP2	1gny / SCOPe / SUPFAM
CAZy	CBM15
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_17/28
structure of fam17 carbohydrate binding module from clostridium cellulovorans
Identifiers
Symbol	CBM_17_28
Pfam	PF03424
Pfam clan	CL0202
InterPro	IPR005086
SCOP2	1g0c / SCOPe / SUPFAM
CAZy	CBM28
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Chitin_bind_1 (CBM18)
crystal structure analysis of crosslinked-wga3/glcnacbeta1,4glcnac complex
Identifiers
Symbol	Chitin_bind_1
Pfam	PF00187
InterPro	IPR001002
PROSITE	PDOC00025
SCOP2	1wgt / SCOPe / SUPFAM
CAZy	CBM18
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_19
Identifiers
Symbol	CBM_19
Pfam	PF03427
Pfam clan	CL0155
InterPro	IPR005089
CAZy	CBM19
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_20
glucoamylase, granular starch-binding domain complex with cyclodextrin, nmr, minimized average structure
Identifiers
Symbol	CBM_20
Pfam	PF00686
Pfam clan	CL0369
InterPro	IPR002044
SCOP2	1cdg / SCOPe / SUPFAM
CAZy	CBM20
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_21
Identifiers
Symbol	CBM_21
Pfam	PF03370
InterPro	IPR005036
CAZy	CBM21
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_25
Identifiers
Symbol	CBM_25
Pfam	PF03423
InterPro	IPR005085
CAZy	CBM25
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM27
structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27
Identifiers
Symbol	CBM27
Pfam	PF09212
InterPro	IPR015295
SCOP2	1oh4 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Chitin_bind_3 (CBM33)
crystal structure of the serratia marcescens chitin-binding protein cbp21 y54a mutant.
Identifiers
Symbol	Chitin_bind_3
Pfam	PF03067
InterPro	IPR004302
CAZy	CBM33
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM_48
crystal structure of glycosyltrehalose trehalohydrolase from sulfolobus solfataricus
Identifiers
Symbol	CBM_48
Pfam	PF02922
Pfam clan	CL0369
InterPro	IPR004193
SCOP2	1bf2 / SCOPe / SUPFAM
CAZy	CBM48
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBM49
Identifiers
Symbol	CBM49
Pfam	PF09478
Pfam clan	CL0203
InterPro	IPR019028
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

CBMs of microbial glycoside hydrolases play a central role in the recycling of photosynthetically fixed carbon through their binding to specific plant structural polysaccharides.^[3] CBMs can recognise both crystalline and amorphous cellulose forms.^[4] CBMs are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. Many putative CBMs have been identified by amino acid sequence alignments but only a few representatives have been shown experimentally to have a carbohydrate-binding function.^[5]

CBM1

Carbohydrate-binding module family 1 (CBM1) consists of 36 amino acids. This domain contains 4 conserved cysteine residues which are involved in the formation of two disulfide bonds.

CBM2

Carbohydrate-binding module family 2 (CBM2) contains two conserved cysteines - one at each extremity of the domain - which have been shown ^[6] to be involved in a disulfide bond. There are also four conserved tryptophans, two of which are involved in cellulose binding.^[7][8][9]

CBM3

Carbohydrate-binding module family 3 (CBM3) is involved in cellulose binding ^[10] and is found associated with a wide range of bacterial glycosyl hydrolases. The structure of this domain is known; it forms a beta sandwich.^[11]

CBM4

Carbohydrate-binding module family 4 (CBM4) includes the two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at the N terminus of the 1,4-beta-glucanase, CenC, from Cellulomonas fimi. These homologous CBMs are distinct in their selectivity for binding amorphous and not crystalline cellulose.^[12] Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1). The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds.^[13] CBM4 and CBM9 are closely related.

CBM5

Carbohydrate-binding module family 5 (CBM5) binds chitin.^[14] CBM5 and CBM12 are distantly related.

CBM6

Carbohydrate-binding module family 6 (CBM6) is unusual in that it contains two substrate-binding sites, cleft A and cleft B. Cellvibrio mixtus endoglucanase 5A contains two CBM6 domains, the CBM6 domain at the C-terminus displays distinct ligand binding specificities in each of the substrate-binding clefts. Both cleft A and cleft B can bind cello-oligosaccharides, laminarin preferentially binds in cleft A, xylooligosaccharides only bind in cleft A and beta1,4,-beta1,3-mixed linked glucans only bind in cleft B.^[15]

CBM9

Carbohydrate-binding module family 9 (CBM9) binds to crystalline cellulose.^[16] CBM4 and CBM9 are closely related.

CBM10

Carbohydrate-binding module family 10 (CBM10) is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains. The dockerin domains are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria.^[17][18]

In anaerobic bacteria that degrade plant cell walls, exemplified by Clostridium thermocellum, the dockerin domains of the catalytic polypeptides can bind equally well to any cohesin from the same organism. More recently, anaerobic fungi, typified by Piromyces equi, have been suggested to also synthesise a cellulosome complex, although the dockerin sequences of the bacterial and fungal enzymes are completely different.^[19] For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. In contrast, all the C. thermocellum cellulosome catalytic components contain a single dockerin domain. The anaerobic bacterial dockerins are homologous to EF hands (calcium-binding motifs) and require calcium for activity whereas the fungal dockerin does not require calcium. Finally, the interaction between cohesin and dockerin appears to be species specific in bacteria, there is almost no species specificity of binding within fungal species and no identified sites that distinguish different species.

The of dockerin from P. equi contains two helical stretches and four short beta-strands which form an antiparallel sheet structure adjacent to an additional short twisted parallel strand. The N- and C-termini are adjacent to each other.^[19]

CBM11

Carbohydrate-binding module family 11 (CBM11) is found in a number of bacterial cellulases. One example is the CBM11 of Clostridium thermocellum Cel26A-Cel5E, this domain has been shown to bind both β-1,4-glucan and β-1,3-1,4-mixed linked glucans.^[20] CBM11 has beta-sandwich structure with a concave side forming a substrate-binding cleft.^[20]

CBM12

Carbohydrate-binding module family 12 (CBM12) comprises two beta-sheets, consisting of two and three antiparallel beta strands respectively. It binds chitin via the aromatic rings of tryptophan residues.^[14] CBM5 and CBM12 are distantly related.

CBM14

Carbohydrate-binding module family 14 (CBM14) is also known as the peritrophin-A domain. It is found in chitin binding proteins, particularly the peritrophic matrix proteins of insects and animal chitinases.^[21][22][23] Copies of the domain are also found in some baculoviruses. It is an extracellular domain that contains six conserved cysteines that probably form three disulfide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.^[21]

CBM15

Carbohydrate-binding module family 15 (CBM15), found in bacterial enzymes, has been shown to bind to xylan and xylooligosaccharides. It has a beta-jelly roll fold, with a groove on the concave surface of one of the beta-sheets.^[3]

CBM17

Carbohydrate-binding module family 17 (CBM17) appears to have a very shallow binding cleft that may be more accessible to cellulose chains in non-crystalline cellulose than the deeper binding clefts of family 4 CBMs.^[24] Sequence and structural conservation in families CBM17 and CBM28 suggests that they have evolved through gene duplication and subsequent divergence.^[4] CBM17 does not compete with CBM28 modules when binding to non-crystalline cellulose. Different CBMs have been shown to bind to different sites in amorphous cellulose, CBM17 and CBM28 recognise distinct non-overlapping sites in amorphous cellulose.^[25]

CBM18

Carbohydrate-binding module family 18 (CBM18) (also known as chitin binding 1 or chitin recognition protein) is found in a number of plant and fungal proteins that bind N-acetylglucosamine (e.g. solanaceous lectins of tomato and potato, plant endochitinases, the wound-induced proteins: hevein, win1 and win2, and the Kluyveromyces lactis killer toxin alpha subunit).^[26] The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits.^[27][28] In chitinases, as well as in the potato wound-induced proteins, this 43-residue domain directly follows the signal sequence and is therefore at the N terminus of the mature protein; in the killer toxin alpha subunit it is located in the central section of the protein.

CBM19

Carbohydrate-binding module family 19 (CBM19), found in fungal chitinases, binds chitin.^[29]

CBM20

Carbohydrate-binding module family 20 (CBM20) binds to starch.^[30][31]

CBM21

Carbohydrate-binding module family 21 (CBM21), found in many eukaryotic proteins involved in glycogen metabolism, binds to glycogen.^[32]

CBM25

Carbohydrate-binding module family 25 (CBM25) binds alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, and granular starch.^[33]

CBM27

Carbohydrate-binding module family 27 (CBM27) binds to beta-1,4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. CBM27 adopts a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom.^[34]

CBM28

Carbohydrate-binding module family 28 (CBM28) does not compete with CBM17 modules when binding to non-crystalline cellulose. Different CBMs have been shown to bind to different sirtes in amorphous cellulose, CBM17 and CBM28 recognise distinct non-overlapping sites in amorphous cellulose. CBM28 has a "beta-jelly roll" topology, which is similar in structure to the CBM17 domains. Sequence and structural conservation in families CBM17 and CBM28 suggests that they have evolved through gene duplication and subsequent divergence.^[4][25]

CBM32

Carbohydrate-binding module family 32 (CBM32) binds to diverse substrates, ranging from plant cell wall polysaccharides to complex glycans.^[35] The module has so far been found in microorganisms, including archea, eubacteria and fungi.^[35] CBM32 adopts a beta-sandwich fold and has a bound metal atom, most often observed to be calcium.^[36] CBM32 modules are associated with catalytic modules such as sialidases, B-N-acetylglucosaminidases, α-N-acetylglucosaminidases, mannanases and galactose oxidases.^[36]

CBM33

Carbohydrate-binding module family 33 (CBM33) is a chitin-binding domain.^[37] It has a budded fibronectin type III fold consisting of two beta-sheets, arranged as a beta-sheet sandwich and a bud consisting of three short helices, located between beta-strands 1 and 2. It binds chitin via conserved polar amino acids.^[38] This domain is found in isolation in baculoviral spheroidin and spindolin proteins.

CBM48

Carbohydrate-binding module family 48 (CBM48) is often found in enzymes containing glycosyl hydrolase family 13 catalytic domains. It is found in a range of enzymes that act on branched substrates i.e. isoamylase, pullulanase and branching enzyme. Isoamylase hydrolyses 1,6-alpha-D-glucosidic branch linkages in glycogen, amylopectin and dextrin; 1,4-alpha-glucan branching enzyme functions in the formation of 1,6-glucosidic linkages of glycogen; and pullulanase is a starch-debranching enzyme. CBM48 binds glycogen.^{[39][40][41][42]}

CBM49

Carbohydrate-binding module family 49 (CBM49) is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose.^[43]

References

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