dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Coprobacter secundus

Lineage

Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Coprobacteraceae; Coprobacter; Coprobacter secundus

CAZyme ID

MGYG000001512_03319

CAZy Family

GH117

CAZyme Description

hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
375	MGYG000001512_19\|CGC38	42539.23	6.7735

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001512	4253015	Isolate	not provided	not provided

Gene Location

Start: 1709020; End: 1710147 Strand: +

Enzyme Prediction help

No EC number prediction in MGYG000001512_03319.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH117	195	350	3.3e-16	0.7630331753554502

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd08994	GH43_62_32_68_117_130-like	6.08e-125	49	352	5	294	Glycosyl hydrolase families: GH43, GH62, GH32, GH68, GH117, CH130. Members of the glycosyl hydrolase families 32, 43, 62, 68, 117 and 130 (GH32, GH43, GH62, GH68, GH117, GH130) all possess 5-bladed beta-propeller domains and comprise clans F and J, as classified by the carbohydrate-active enzymes database (CAZY). Clan F consists of families GH43 and GH62. GH43 includes beta-xylosidases (EC 3.2.1.37), beta-xylanases (EC 3.2.1.8), alpha-L-arabinases (EC 3.2.1.99), and alpha-L-arabinofuranosidases (EC 3.2.1.55), using aryl-glycosides as substrates, while family GH62 contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose sidechains from xylans. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Clan J consists of families GH32 and GH68. GH32 comprises sucrose-6-phosphate hydrolases, invertases (EC 3.2.1.26), inulinases (EC 3.2.1.7), levanases (EC 3.2.1.65), eukaryotic fructosyltransferases, and bacterial fructanotransferases while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Members of this clan are retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) that catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. Structures of all families in the two clans manifest a funnel-shaped active site that comprises two subsites with a single route for access by ligands. Also included in this superfamily are GH117 enzymes that have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate, and GH130 that are phosphorylases and hydrolases for beta-mannosides, involved in the bacterial utilization of mannans or N-linked glycans.
cd08772	GH43_62_32_68_117_130	4.50e-22	58	313	1	221	Glycosyl hydrolase families: GH43, GH62, GH32, GH68, GH117, CH130. Members of the glycosyl hydrolase families 32, 43, 62, 68, 117 and 130 (GH32, GH43, GH62, GH68, GH117, GH130) all possess 5-bladed beta-propeller domains and comprise clans F and J, as classified by the carbohydrate-active enzymes database (CAZY). Clan F consists of families GH43 and GH62. GH43 includes beta-xylosidases (EC 3.2.1.37), beta-xylanases (EC 3.2.1.8), alpha-L-arabinases (EC 3.2.1.99), and alpha-L-arabinofuranosidases (EC 3.2.1.55), using aryl-glycosides as substrates, while family GH62 contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose sidechains from xylans. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Clan J consists of families GH32 and GH68. GH32 comprises sucrose-6-phosphate hydrolases, invertases (EC 3.2.1.26), inulinases (EC 3.2.1.7), levanases (EC 3.2.1.65), eukaryotic fructosyltransferases, and bacterial fructanotransferases while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Members of this clan are retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) that catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. Structures of all families in the two clans manifest a funnel-shaped active site that comprises two subsites with a single route for access by ligands. Also included in this superfamily are GH117 enzymes that have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate, and GH130 that are phosphorylases and hydrolases for beta-mannosides, involved in the bacterial utilization of mannans or N-linked glycans.
cd08992	GH117	1.28e-19	60	255	26	228	Glycosyl hydrolase family 117 (GH117). This glycoside hydrolase 117 (GH117) family includes alpha-1,3-L-neoagarooligosaccharide hydrolase (EC 3.2.1.-); alpha-1,3-L-neoagarobiase/neoagarobiose hydrolase (NABH, EC 3.2.1.-). In the agarolytic pathway, in order to metabolize agar, NABH is an essential enzyme because it converts alpha-neoagarobiose (O-3,6-anhydro-alpha-l-galactopyranosyl-(1,3)-d-galactose) into fermentable monosaccharides (d-galactose and 3,6-anhydro-l-galactose). Thus, these enzymes have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate. This family includes Zobellia galactanivorans enzymes, Zg4663 and Zg3615 (also known as ZgAhgA and ZgAhgB, respectively) that have been shown to have similar activity on unsubstituted agarose oligosaccharides while Zg3597 has been shown to be inactive, possibly due to differences in dimerization conformation, active-site structure and function. GH117 shares distant sequence similarity with families GH43 and GH32. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd08991	GH43_HoAraf43-like	4.17e-07	60	200	110	232	Glycosyl hydrolase family 43 protein such as Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (HoAraf43;Hore_20580). This glycosyl hydrolase family 43 (GH43) subgroup includes Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (EC 3.2.1.55) (HoAraf43;Hore_20580). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. This GH43_ HoAraf43-like subgroup includes enzymes that have been annotated as having xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd08999	GH43_ABN-like	1.33e-06	120	221	177	256	Glycosyl hydrolase family 43 protein such as endo-alpha-L-arabinanase. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
BCI62492.1	5.97e-292	1	375	1	375
QUT89204.1	2.42e-211	1	374	1	375
ALJ59764.1	2.42e-211	1	374	1	375
QUT61435.1	4.09e-208	1	374	1	374
QUT37262.1	4.09e-208	1	374	1	374

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3R4Y_A	7.45e-10	60	250	54	252	Crystalstructure of alpha-neoagarobiose hydrolase (ALPHA-NABH) from Saccharophagus degradans 2-40 [Saccharophagus degradans 2-40],3R4Y_B Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) from Saccharophagus degradans 2-40 [Saccharophagus degradans 2-40],3R4Z_A Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with alpha-d-galactopyranose from Saccharophagus degradans 2-40 [Saccharophagus degradans 2-40],3R4Z_B Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with alpha-d-galactopyranose from Saccharophagus degradans 2-40 [Saccharophagus degradans 2-40]
5TA7_A	6.03e-09	60	250	90	288	Crystalstructure of BuGH117Bwt [Bacteroides uniformis],5TA7_B Crystal structure of BuGH117Bwt [Bacteroides uniformis],5TA9_A Crystal structure of BuGH117Bwt in complex with neoagarobiose [Bacteroides uniformis],5TA9_B Crystal structure of BuGH117Bwt in complex with neoagarobiose [Bacteroides uniformis],5TA9_C Crystal structure of BuGH117Bwt in complex with neoagarobiose [Bacteroides uniformis],5TA9_D Crystal structure of BuGH117Bwt in complex with neoagarobiose [Bacteroides uniformis]
3P2N_A	2.44e-06	120	250	165	297	Discoveryand structural characterization of a new glycoside hydrolase family abundant in coastal waters that was annotated as 'hypothetical protein' [Zobellia galactanivorans],3P2N_B Discovery and structural characterization of a new glycoside hydrolase family abundant in coastal waters that was annotated as 'hypothetical protein' [Zobellia galactanivorans]