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60  structures 465  species 2  interactions 1755  sequences 402  architectures

Family: CBM_6 (PF03422)

Summary: Carbohydrate binding module (family 6)

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Carbohydrate-binding module Edit Wikipedia article

CBM_1
PDB 1azj EBI.jpg
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
SCOP 1cel
SUPERFAMILY 1cel
CAZy CBM1
CBM_2
PDB 1exg EBI.jpg
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
SCOP 1exg
SUPERFAMILY 1exg
CAZy CBM2
CBM_3
PDB 1g43 EBI.jpg
crystal structure of a family iiia cbd from clostridium cellulolyticum
Identifiers
Symbol CBM_3
Pfam PF00942
Pfam clan CL0203
InterPro IPR001956
SCOP 1nbc
SUPERFAMILY 1nbc
CAZy CBM3
CBM_5/12
PDB 1ur9 EBI.jpg
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
SCOP 1ed7
SUPERFAMILY 1ed7
CAZy CBM12
CBM_6
PDB 1uxx EBI.jpg
cbm6ct from clostridium thermocellum in complex with xylopentaose
Identifiers
Symbol CBM_6
Pfam PF03422
Pfam clan CL0202
InterPro IPR005084
SCOP 1gmm
SUPERFAMILY 1gmm
CAZy CBM6
CBM_4/9
PDB 1gui EBI.jpg
cbm4 structure and function
Identifiers
Symbol CBM_4_9
Pfam PF02018
Pfam clan CL0202
InterPro IPR003305
SCOP 1ulp
SUPERFAMILY 1ulp
CAZy CBM22
CBM_10
PDB 1qld EBI.jpg
solution structure of type x cbm
Identifiers
Symbol CBM_10
Pfam PF02013
InterPro IPR002883
SCOP 1qld
SUPERFAMILY 1qld
CAZy CBM10
CBM_11
PDB 1v0a EBI.jpg
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
CBM_14
Identifiers
Symbol CBM_14
Pfam PF01607
Pfam clan CL0155
InterPro IPR002557
SCOP 1dqc
SUPERFAMILY 1dqc
CAZy CBM14
CBM_15
PDB 1gny EBI.jpg
xylan-binding module cbm15
Identifiers
Symbol CBM_15
Pfam PF03426
Pfam clan CL0202
InterPro IPR005088
SCOP 1gny
SUPERFAMILY 1gny
CAZy CBM15
CBM_17/28
PDB 1j83 EBI.jpg
structure of fam17 carbohydrate binding module from clostridium cellulovorans
Identifiers
Symbol CBM_17_28
Pfam PF03424
Pfam clan CL0202
InterPro IPR005086
SCOP 1g0c
SUPERFAMILY 1g0c
CAZy CBM28
Chitin_bind_1 (CBM18)
PDB 1k7u EBI.jpg
crystal structure analysis of crosslinked-wga3/glcnacbeta1,4glcnac complex
Identifiers
Symbol Chitin_bind_1
Pfam PF00187
InterPro IPR001002
PROSITE PDOC00025
SCOP 1wgt
SUPERFAMILY 1wgt
CAZy CBM18
CBM_19
Identifiers
Symbol CBM_19
Pfam PF03427
Pfam clan CL0155
InterPro IPR005089
CAZy CBM19
CBM_20
PDB 1ac0 EBI.jpg
glucoamylase, granular starch-binding domain complex with cyclodextrin, nmr, minimized average structure
Identifiers
Symbol CBM_20
Pfam PF00686
Pfam clan CL0369
InterPro IPR002044
SCOP 1cdg
SUPERFAMILY 1cdg
CAZy CBM20
CBM_21
Identifiers
Symbol CBM_21
Pfam PF03370
InterPro IPR005036
CAZy CBM21
CBM_25
Identifiers
Symbol CBM_25
Pfam PF03423
InterPro IPR005085
CAZy CBM25
CBM27
PDB 1of3 EBI.jpg
structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27
Identifiers
Symbol CBM27
Pfam PF09212
InterPro IPR015295
SCOP 1oh4
SUPERFAMILY 1oh4
Chitin_bind_3 (CBM33)
PDB 2ben EBI.jpg
crystal structure of the serratia marcescens chitin-binding protein cbp21 y54a mutant.
Identifiers
Symbol Chitin_bind_3
Pfam PF03067
InterPro IPR004302
CAZy CBM33
CBM_48
PDB 1eha EBI.jpg
crystal structure of glycosyltrehalose trehalohydrolase from sulfolobus solfataricus
Identifiers
Symbol CBM_48
Pfam PF02922
Pfam clan CL0369
InterPro IPR004193
SCOP 1bf2
SUPERFAMILY 1bf2
CAZy CBM48
CBM49
Identifiers
Symbol CBM49
Pfam PF09478
Pfam clan CL0203
InterPro IPR019028

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]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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

CBM6[edit]

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.[15]

CBM9[edit]

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

CBM10[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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.[24]

CBM17[edit]

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.[25] 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 sirtes in amorphous cellulose, CBM17 and CBM28 recognise distinct non-overlapping sites in amorphous cellulose.[26]

CBM18[edit]

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).[27] The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits.[28][29] 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[edit]

Carbohydrate-binding module family 19 (CBM19), found in fungal chitinases, binds chitin.[30]

CBM20[edit]

Carbohydrate-binding module family 20 (CBM20) binds to starch.[31][32]

CBM21[edit]

Carbohydrate-binding module family 21 (CBM21), found in many eukaryotic proteins involved in glycogen metabolism, binds to glycogen.[33]

CBM25[edit]

Carbohydrate-binding module family 25 (CBM25) binds alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, and granular starch.[34]

CBM27[edit]

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.[35]

CBM28[edit]

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][26]

CBM33[edit]

Carbohydrate-binding module family 33 (CBM33) is a chitin-binding domain.[36] 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.[37] This domain is found in isolation in baculoviral spheroidin and spindolin proteins.

CBM48[edit]

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.[38][39][40][41]

CBM49[edit]

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.[42]

References[edit]

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  2. ^ Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.; Bernard, T.; Lombard, V.; Henrissat, B. (2009). "The Carbohydrate-Active EnZymes database (CAZy): An expert resource for Glycogenomics". Nucleic Acids Research 37 (Database issue): D233–D238. doi:10.1093/nar/gkn663. PMC 2686590. PMID 18838391.  edit
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  4. ^ a b c Jamal S, Nurizzo D, Boraston AB, Davies GJ (May 2004). "X-ray crystal structure of a non-crystalline cellulose-specific carbohydrate-binding module: CBM28". J. Mol. Biol. 339 (2): 253–8. doi:10.1016/j.jmb.2004.03.069. PMID 15136030. 
  5. ^ Roske Y, Sunna A, Pfeil W, Heinemann U (July 2004). "High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose". J. Mol. Biol. 340 (3): 543–54. doi:10.1016/j.jmb.2004.04.072. PMID 15210353. 
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  14. ^ a b 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.  edit
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  16. ^ 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.  edit
  17. ^ Millward-Sadler SJ, Davidson K, Hazlewood GP, Black GW, Gilbert HJ, Clarke JH (November 1995). "Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus". Biochem. J. 312 (1): 39–48. PMC 1136224. PMID 7492333. 
  18. ^ Fanutti C, Ponyi T, Black GW, Hazlewood GP, Gilbert HJ (December 1995). "The conserved noncatalytic 40-residue sequence in cellulases and hemicellulases from anaerobic fungi functions as a protein docking domain". J. Biol. Chem. 270 (49): 29314–22. PMID 7493964. 
  19. ^ a b 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. 
  20. ^ a b 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.  edit
  21. ^ a b 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. PMID 9651363. 
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  23. ^ 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. 
  24. ^ 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.  edit
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  26. ^ a b 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.  edit
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  28. ^ Butler AR, O'Donnell RW, Martin VJ, Gooday GW, Stark MJ (July 1991). "Kluyveromyces lactis toxin has an essential chitinase activity". Eur. J. Biochem. 199 (2): 483–8. doi:10.1111/j.1432-1033.1991.tb16147.x. PMID 2070799. 
  29. ^ Lerner DR, Raikhel NV (June 1992). "The gene for stinging nettle lectin (Urtica dioica agglutinin) encodes both a lectin and a chitinase". J. Biol. Chem. 267 (16): 11085–91. PMID 1375935. 
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  32. ^ Oyama, T.; Kusunoki, M.; Kishimoto, Y.; Takasaki, Y.; Nitta, Y. (1999). "Crystal structure of beta-amylase from Bacillus cereus var. Mycoides at 2.2 a resolution". Journal of biochemistry 125 (6): 1120–1130. doi:10.1093/oxfordjournals.jbchem.a022394. PMID 10348915.  edit
  33. ^ Armstrong, C. G.; Doherty, M. J.; Cohen, P. T. (1998). "Identification of the separate domains in the hepatic glycogen-targeting subunit of protein phosphatase 1 that interact with phosphorylase a, glycogen and protein phosphatase 1". The Biochemical journal 336 (3): 699–704. PMC 1219922. PMID 9841883.  edit
  34. ^ Boraston, A. B.; Healey, M.; Klassen, J.; Ficko-Blean, E.; Lammerts Van Bueren, A.; Law, V. (2005). "A Structural and Functional Analysis of  -Glucan Recognition by Family 25 and 26 Carbohydrate-binding Modules Reveals a Conserved Mode of Starch Recognition". Journal of Biological Chemistry 281 (1): 587–598. doi:10.1074/jbc.M509958200. PMID 16230347.  edit
  35. ^ Boraston AB, Revett TJ, Boraston CM, Nurizzo D, Davies GJ (June 2003). "Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27". Structure 11 (6): 665–75. doi:10.1016/S0969-2126(03)00100-X. PMID 12791255. 
  36. ^ Schnellmann, J.; Zeltins, A.; Blaak, H.; Schrempf, H. (1994). "The novel lectin-like protein CHB1 is encoded by a chitin-inducible Streptomyces olivaceoviridis gene and binds specifically to crystalline alpha-chitin of fungi and other organisms". Molecular microbiology 13 (5): 807–819. doi:10.1111/j.1365-2958.1994.tb00473.x. PMID 7815940.  edit
  37. ^ Vaaje-Kolstad, G.; Houston, D. R.; Riemen, A. H.; Eijsink, V. G.; Van Aalten, D. M. (2005). "Crystal Structure and Binding Properties of the Serratia marcescens Chitin-binding Protein CBP21". Journal of Biological Chemistry 280 (12): 11313–11319. doi:10.1074/jbc.M407175200. PMID 15590674.  edit
  38. ^ Katsuya, Y.; Mezaki, Y.; Kubota, M.; Matsuura, Y. (1998). "Three-dimensional structure of Pseudomonas isoamylase at 2.2 Å resolution1". Journal of Molecular Biology 281 (5): 885–897. doi:10.1006/jmbi.1998.1992. PMID 9719642.  edit
  39. ^ Wiatrowski, H. A.; Van Denderen, B. J.; Berkey, C. D.; Kemp, B. E.; Stapleton, D.; Carlson, M. (2004). "Mutations in the gal83 glycogen-binding domain activate the snf1/gal83 kinase pathway by a glycogen-independent mechanism". Molecular and Cellular Biology 24 (1): 352–361. PMC 303368. PMID 14673168.  edit
  40. ^ 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.  edit
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External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR000254

This article incorporates text from the public domain Pfam and InterPro IPR002883

This article incorporates text from the public domain Pfam and InterPro IPR005087

This article incorporates text from the public domain Pfam and InterPro IPR002557

This article incorporates text from the public domain Pfam and InterPro IPR005088

This article incorporates text from the public domain Pfam and InterPro IPR005086

This article incorporates text from the public domain Pfam and InterPro IPR005089

This article incorporates text from the public domain Pfam and InterPro IPR001919

This article incorporates text from the public domain Pfam and InterPro IPR002044

This article incorporates text from the public domain Pfam and InterPro IPR005036

This article incorporates text from the public domain Pfam and InterPro IPR005085

This article incorporates text from the public domain Pfam and InterPro IPR015295

This article incorporates text from the public domain Pfam and InterPro IPR001956

This article incorporates text from the public domain Pfam and InterPro IPR004193

This article incorporates text from the public domain Pfam and InterPro IPR019028

This article incorporates text from the public domain Pfam and InterPro IPR003305

This article incorporates text from the public domain Pfam and InterPro IPR003610

This article incorporates text from the public domain Pfam and InterPro IPR005084

This article incorporates text from the public domain Pfam and InterPro IPR001002

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 module (family 6) Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005084

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].

This entry represents CAZY which was previously known as cellulose-binding domain family VI (CBD VI). CBM6 bind to amorphous cellulose, xylan, mixed beta-(1,3)(1,4)glucan and beta-1,3-glucan[PUBMED:15501830, PUBMED:15004011, PUBMED:15010454].

CBM6 adopts a classic lectin-like beta-jelly roll fold, predominantly consisting of five antiparallel beta-strands on one face and four antiparallel beta-strands on the other face. It contains two potential ligand binding sites, named respectively cleft A and B. These clefts include aromatic residues which are probably involved in the substrate binding. The cleft B is located on the concave surface of one beta-sheet, and the cleft A on one edge of the protein between the loop that connects the inner and outer beta-sheets of the jellyroll fold [PUBMED:11673472]. The multiple binding clefts confer the extensive range of specificities displayed by the domain [PUBMED:15501830, PUBMED:15004011, PUBMED:15010454].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 27 members:

Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH Sad1_UNC XRCC1_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(41)
Full
(1755)
Representative proteomes NCBI
(1810)
Meta
(331)
RP15
(338)
RP35
(629)
RP55
(686)
RP75
(713)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(41)
Full
(1755)
Representative proteomes NCBI
(1810)
Meta
(331)
RP15
(338)
RP35
(629)
RP55
(686)
RP75
(713)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(41)
Full
(1755)
Representative proteomes NCBI
(1810)
Meta
(331)
RP15
(338)
RP35
(629)
RP55
(686)
RP75
(713)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1231 (release 6.6)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 41
Number in full: 1755
Average length of the domain: 121.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 17.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.2 21.0
Noise cut-off 20.9 20.9
Model length: 125
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Interactions

There are 2 interactions for this family. More...

Glyco_hydro_11 CBM_6

Structures

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_6 domain has been found. There are 60 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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