Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality.
The actual alignment was detected with superfamily member cd04083:
Pssm-ID: 449372 Cd Length: 125 Bit Score: 62.27 E-value: 1.66e-11
Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes ...
759-884
1.66e-11
Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes EGD-e. These CBM35s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. GH31 has a wide range of hydrolytic activities such as alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, or alpha-1,4-glucan lyase, cleaving a terminal carbohydrate moiety from a substrate that may be a starch or a glycoprotein. Most characterized GH31 enzymes are alpha-glucosidases.
Pssm-ID: 271149 Cd Length: 125 Bit Score: 62.27 E-value: 1.66e-11
Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme Swiss:P35573. ...
230-576
1.72e-07
Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme Swiss:P35573. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homolog Swiss:O93808 that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33).
Pssm-ID: 428822 Cd Length: 370 Bit Score: 54.26 E-value: 1.72e-07
Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes ...
759-884
1.66e-11
Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446; This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes EGD-e. These CBM35s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. GH31 has a wide range of hydrolytic activities such as alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, or alpha-1,4-glucan lyase, cleaving a terminal carbohydrate moiety from a substrate that may be a starch or a glycoprotein. Most characterized GH31 enzymes are alpha-glucosidases.
Pssm-ID: 271149 Cd Length: 125 Bit Score: 62.27 E-value: 1.66e-11
Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme Swiss:P35573. ...
230-576
1.72e-07
Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme Swiss:P35573. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homolog Swiss:O93808 that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33).
Pssm-ID: 428822 Cd Length: 370 Bit Score: 54.26 E-value: 1.72e-07
Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, ...
759-872
1.95e-06
Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes, including periplasmic component of ABC-type sugar transport system involved in carbohydrate transport and metabolism, and several glycoside hydrolase (GH) domains, including GH26. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB35s belonging to this family are mannanase A from Clostridium thermocellum (GH26), Man26B from Paenibacillus sp. BME-14 (GH26), and the multifunctional Cel44C-Man26A from Paenibacillus polymyxa GS01 (which has two GH domains, GH44 and GH26). GH26 mainly includes mannan endo-1,4-beta-mannosidase which hydrolyzes 1,4-beta-D-linkages in mannans, galacto-mannans, glucomannans, and galactoglucomannans, but displays little activity towards other plant cell wall polysaccharides. A few proteins belonging to this family have additional CBM3 domains; these CBM3s are not found in the CBM6-CBM35-CBM36_like superfamily.
Pssm-ID: 271152 Cd Length: 119 Bit Score: 47.60 E-value: 1.95e-06
Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes ...
767-815
1.50e-03
Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans; This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included in this family are CBM35s of pectate lyases, including pectate lyase 10A from Cellvibrio japonicas, these enzymes release delta-4,5-anhydrogalaturonic acid (delta4,5-GalA) from pectin, thus identifying a signature molecule for plant cell wall degradation. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. Some CBM35s bind their ligands in a calcium-dependent manner, especially those binding uronic acids.
Pssm-ID: 271148 Cd Length: 124 Bit Score: 39.47 E-value: 1.50e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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