Summary: Carbohydrate binding domain (family 25)
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Carbohydrate-binding module Edit Wikipedia article
three-dimensional structures of three engineered cellulose-binding domains of cellobiohydrolase i from trichoderma reesei, nmr, 18 structures
solution structure of a cellulose binding domain from cellulomonas fimi by nuclear magnetic resonance spectroscopy
crystal structure of a family iiia cbd from clostridium cellulolyticum
interactions of a family 18 chitinase with the designed inhibitor hm508, and its degradation product, chitobiono-delta-lactone
cbm6ct from clostridium thermocellum in complex with xylopentaose
cbm4 structure and function
solution structure of type x cbm
family 11 carbohydrate-binding module of cellulosomal cellulase lic26a-cel5e of clostridium thermocellum
xylan-binding module cbm15
structure of fam17 carbohydrate binding module from clostridium cellulovorans
crystal structure analysis of crosslinked-wga3/glcnacbeta1,4glcnac complex
glucoamylase, granular starch-binding domain complex with cyclodextrin, nmr, minimized average structure
structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27
crystal structure of the serratia marcescens chitin-binding protein cbp21 y54a mutant.
crystal structure of glycosyltrehalose trehalohydrolase from sulfolobus solfataricus
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. 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.
CBMs of microbial glycoside hydrolases play a central role in the recycling of photosynthetically fixed carbon through their binding to specific plant structural polysaccharides. CBMs can recognise both crystalline and amorphous cellulose forms. 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.
Carbohydrate-binding module family 2 (CBM2) contains two conserved cysteines - one at each extremity of the domain - which have been shown  to be involved in a disulfide bond. There are also four conserved tryptophans, two of which are involved in cellulose binding.
Carbohydrate-binding module family 3 (CBM3) is involved in cellulose binding  and is found associated with a wide range of bacterial glycosyl hydrolases. The structure of this domain is known; it forms a beta sandwich.
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. 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. CBM4 and CBM9 are closely related.
Carbohydrate-binding module family 5 (CBM5) binds chitin. CBM5 and CBM12 are distantly related.
Carbohydrate-binding module family 6 (CBM6) is unusual in that is 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 sustrate-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.
Carbohydrate-binding module family 9 (CBM9) binds to crystalline cellulose. CBM4 and CBM9 are closely related.
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.
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. 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.
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. CBM11 has beta-sandwich structure with a concave side forming a substrate-binding cleft.
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. CBM5 and CBM12 are distantly related.
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. 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.
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.
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. Sequence and structural conservation in families CBM17 and CBM28 suggests that they have evolved through gene duplication and subsequent divergence. CBM17 does not compete with CBM28 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.
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). The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits. 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.
Carbohydrate-binding module family 25 (CBM25) binds alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, and granular starch.
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.
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.
Carbohydrate-binding module family 33 (CBM33) is a chitin-binding domain. 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. This domain is found in isolation in baculoviral spheroidin and spindolin proteins.
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.
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- Johnson PE, Joshi MD, Tomme P, Kilburn DG, McIntosh LP (November 1996). "Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy". Biochemistry 35 (45): 14381–94. doi:10.1021/bi961612s. PMID 8916925.
- Akagi, K. -I.; Watanabe, J.; Hara, M.; Kezuka, Y.; Chikaishi, E.; Yamaguchi, T.; Akutsu, H.; Nonaka, T.; Watanabe, T.; Ikegami, T. (2006). "Identification of the Substrate Interaction Region of the Chitin-Binding Domain of Streptomyces griseus Chitinase C". Journal of Biochemistry 139 (3): 483–493. doi:10.1093/jb/mvj062. PMID 16567413.
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- Winterhalter, C.; Heinrich, P.; Candussio, A.; Wich, G.; Liebl, W. (1995). "Identification of a novel cellulose-binding domain within the multidomain 120 kDa xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima". Molecular microbiology 15 (3): 431–444. doi:10.1111/j.1365-2958.1995.tb02257.x. PMID 7783614.
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- Raghothama S, Eberhardt RY, Simpson P, Wigelsworth D, White P, Hazlewood GP, Nagy T, Gilbert HJ, Williamson MP (September 2001). "Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi". Nat. Struct. Biol. 8 (9): 775–8. doi:10.1038/nsb0901-775. PMID 11524680.
- Carvalho, A. L.; Goyal, A.; Prates, J. A.; Bolam, D. N.; Gilbert, H. J.; Pires, V. M.; Ferreira, L. M.; Planas, A.; Romão, M. J.; Fontes, C. M. (2004). "The Family 11 Carbohydrate-binding Module of Clostridium thermocellum Lic26A-Cel5E Accommodates -1,4- and -1,3-1,4-Mixed Linked Glucans at a Single Binding Site". Journal of Biological Chemistry 279 (33): 34785–34793. doi:10.1074/jbc.M405867200. PMID 15192099.
- Shen Z, Jacobs-Lorena M (July 1998). "A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin. Cloning, expression, and characterization". J. Biol. Chem. 273 (28): 17665–70. doi:10.1074/jbc.273.28.17665. PMID 9651363.
- Elvin CM, Vuocolo T, Pearson RD, East IJ, Riding GA, Eisemann CH, Tellam RL (April 1996). "Characterization of a major peritrophic membrane protein, peritrophin-44, from the larvae of Lucilia cuprina. cDNA and deduced amino acid sequences". J. Biol. Chem. 271 (15): 8925–35. doi:10.1074/jbc.271.15.8925. PMID 8621536.
- Casu R, Eisemann C, Pearson R, Riding G, East I, Donaldson A, Cadogan L, Tellam R (August 1997). "Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a mammalian host". Proc. Natl. Acad. Sci. U.S.A. 94 (17): 8939–44. doi:10.1073/pnas.94.17.8939. PMC 22971. PMID 9256413.
- Szabo, L.; Jamal, S.; Xie, H.; Charnock, S. J.; Bolam, D. N.; Gilbert, H. J.; Davies, G. J. (2001). "Structure of a Family 15 Carbohydrate-binding Module in Complex with Xylopentaose. EVIDENCE THAT XYLAN BINDS IN AN APPROXIMATE 3-FOLD HELICAL CONFORMATION". Journal of Biological Chemistry 276 (52): 49061–49065. doi:10.1074/jbc.M109558200. PMID 11598143.
- Notenboom V, Boraston AB, Chiu P, Freelove AC, Kilburn DG, Rose DR (December 2001). "Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study". J. Mol. Biol. 314 (4): 797–806. doi:10.1006/jmbi.2001.5153. PMID 11733998.
- Jamal, S.; Nurizzo, D.; Boraston, A. B.; Davies, G. J. (2004). "X-ray Crystal Structure of a Non-crystalline Cellulose-specific Carbohydrate-binding Module: CBM28". Journal of Molecular Biology 339 (2): 253–258. doi:10.1016/j.jmb.2004.03.069. PMID 15136030.
- Wright HT, Sandrasegaram G, Wright CS (September 1991). "Evolution of a family of N-acetylglucosamine binding proteins containing the disulfide-rich domain of wheat germ agglutinin". J. Mol. Evol. 33 (3): 283–94. doi:10.1007/bf02100680. PMID 1757999.
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- Penninga, D.; Van Der Veen, B. A.; Knegtel, R. M.; Van Hijum, S. A.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W.; Dijkhuizen, L. (1996). "The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251". The Journal of Biological Chemistry 271 (51): 32777–32784. doi:10.1074/jbc.271.51.32777. PMID 8955113.
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- Polekhina, G.; Gupta, A.; Michell, B. J.; Van Denderen, B.; Murthy, S.; Feil, S. C.; Jennings, I. G.; Campbell, D. J.; Witters, L. A.; Parker, M. W.; Kemp, B. E.; Stapleton, D. (2003). "AMPK beta subunit targets metabolic stress sensing to glycogen". Current biology : CB 13 (10): 867–871. doi:10.1016/S0960-9822(03)00292-6. PMID 12747837.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Carbohydrate binding domain (family 25) Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR005085
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.
CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [PUBMED:3338453, PUBMED:3134347]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.
Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see [PUBMED:15214846].
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|Molecular function||starch binding (GO:2001070)|
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Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||30|
|Number in full:||440|
|Average length of the domain:||84.90 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||18.88 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CBM_25 domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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