1QWN
GOLGI ALPHA-MANNOSIDASE II Covalent Intermediate Complex with 5-fluoro-gulosyl-fluoride
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1qwna1 | All alpha proteins | immunoglobulin/albumin-binding domain-like | Families 57/38 glycoside transferase middle domain | alpha-mannosidase, domain 2 | Golgi alpha-mannosidase II | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
A | d1qwna2 | All beta proteins | Supersandwich | Galactose mutarotase-like | alpha-mannosidase, C-terminal domain | Golgi alpha-mannosidase II | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
A | d1qwna3 | Alpha and beta proteins (a/b) | 7-stranded beta/alpha barrel | Glycoside hydrolase/deacetylase | alpha-mannosidase | Golgi alpha-mannosidase II | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Families 57/38 glycoside transferase middle domain | 8039561 | 3000997 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Galactose mutarotase-like | 8039564 | 3000035 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Glycoside hydrolase/deacetylase | 8039566 | 3001025 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | KOG1958 | e1qwnA2 | A: beta sandwiches | X: Glycosyl hydrolase domain-like | H: Glycosyl hydrolase domain (From Topology) | T: Glycosyl hydrolase domain | F: KOG1958 | ECOD (1.6) |
A | KOG1959 | e1qwnA1 | A: beta sandwiches | X: Glycosyl hydrolase domain-like | H: Glycosyl hydrolase domain (From Topology) | T: Glycosyl hydrolase domain | F: KOG1959 | ECOD (1.6) |
A | Glyco_hydro_38C_1st_1 | e1qwnA4 | A: beta sandwiches | X: Glycosyl hydrolase domain-like | H: supersandwich (From Topology) | T: supersandwich | F: Glyco_hydro_38C_1st_1 | ECOD (1.6) |
A | Alpha-mann_mid | e1qwnA5 | A: alpha bundles | X: immunoglobulin/albumin-binding domain-like | H: Families 57/38 glycoside transferase middle domain (From Topology) | T: Families 57/38 glycoside transferase middle domain | F: Alpha-mann_mid | ECOD (1.6) |
A | Glyco_hydro_38 | e1qwnA6 | A: a/b barrels | X: TIM beta/alpha-barrel | H: Glycoside hydrolase/deacetylase (From Topology) | T: Glycoside hydrolase/deacetylase | F: Glyco_hydro_38 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.20.110.10 | Alpha Beta | Alpha-Beta Barrel | 7-stranded beta/alpha barrel | Glycoside hydrolase 38, N terminal domain | CATH (4.3.0) |
A | 1.20.1270.50 | Mainly Alpha | Up-down Bundle | Substrate Binding Domain Of Dnak | Chain:A | CATH (4.3.0) |
A | 2.60.40.1180 | Mainly Beta | Sandwich | Immunoglobulin-like | Golgi alpha-mannosidase II | CATH (4.3.0) |
A | 2.70.98.30 | Mainly Beta | Distorted Sandwich | Beta-galactosidase | Chain A, domain 5 | CATH (4.3.0) |
A | 2.60.40.1360 | Mainly Beta | Sandwich | Immunoglobulin-like | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF18230 | Glycosyl hydrolases family 38 C-terminal sub-domain (Glyc_hyd_38C_2) | Glycosyl hydrolases family 38 C-terminal sub-domain | This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mech ... | Domain | |
PF01074 | Glycosyl hydrolases family 38 N-terminal domain (Glyco_hydro_38N) | Glycosyl hydrolases family 38 N-terminal domain | Glycosyl hydrolases are key enzymes of carbohydrate metabolism. | Domain | |
PF09261 | Alpha mannosidase middle domain (Alpha-mann_mid) | Alpha mannosidase middle domain | Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase [1]. | Domain | |
PF21260 | Lysosomal alpha-mannosidase-like, central domain (Laman-like_dom) | Lysosomal alpha-mannosidase-like, central domain | This domain is found in Lysosomal alpha-mannosidase from Bos taurus (Laman) and similar proteins from eukaryotes. This protein is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. Laman, which belongs to th ... | Domain | |
PF07748 | Glycosyl hydrolases family 38 C-terminal domain (Glyco_hydro_38C) | Glycosyl hydrolases family 38 C-terminal domain | Glycosyl hydrolases are key enzymes of carbohydrate metabolism. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR015341 | Glycoside hydrolase family 38, central domain | Domain | |
IPR041566 | Alpha-mannosidase 2, C-terminal sub-domain | Domain | |
IPR013780 | Glycosyl hydrolase, all-beta | Homologous Superfamily | |
IPR027291 | Glycoside hydrolase 38, N-terminal domain superfamily | Homologous Superfamily | |
IPR037094 | Glycoside hydrolase family 38, central domain superfamily | Homologous Superfamily | |
IPR028995 | Glycoside hydrolase families 57/38, central domain superfamily | Homologous Superfamily | |
IPR050843 | Glycosyl Hydrolase Family 38 | Family | |
IPR048534 | Lysosomal alpha-mannosidase-like, central domain | Domain | |
IPR011330 | Glycoside hydrolase/deacetylase, beta/alpha-barrel | Homologous Superfamily | |
IPR011682 | Glycosyl hydrolase family 38, C-terminal | Domain | |
IPR000602 | Glycoside hydrolase family 38, N-terminal domain | Domain | |
IPR011013 | Galactose mutarotase-like domain superfamily | Homologous Superfamily |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase M-CSA #793 | Golgi alpha-mannosidase II (dGMII) from Drosophila melanogaster is a member of the glycosyl hydrolase family 38. It catalyses the hydrolysis of the terminal 1,3- and 1,6-linked alpha-D-mannose (Man) residues in the mannosyl-oligosaccharide Man(5)(GlcNAc)(3) producing Man(3)(GlcNAc)(3). GlcNAc stands for N-acetylglucosamine. The enzyme has a high degree of conservation of sequence among many eukaryotes. Inhibition of the human GMII may be helpful in the treatmant of breast, colon or skin cancer. GMII is involved in the N-linked glycosylation pathway which begins in the endoplasmic reticulum where an oligosaccharide is attached to an asparagine residue on a nascent polypeptide. GMII is located in the Golgi apparatus and is one of the glycosyl hydrolases involved in trimming the oligosaccharide. The active site of GMII consitsis of a ctalytic site, a holding site, and an anchor site. Initially the alpha1,6-linked mannose residue of the substrate binds in the catalytic site while the alpha1,3-linked mannose bind in the holding site. A terminal N-acetylglucosamine residue of the substrate binds in the holding site and helps orient the substrate for the hydrolysis reaction. The holding site cannot accommodate the alpha1,6-linked residue without displacing the terminal N-acetylglucosamine from the anchor site. This ensures that the alpha1,6 bond is hydrolysed before the alpha1,3 bond. In in vitro studies dGMII shows an 80-fold preference for substrates containing a nonreducing beta(1,2)-linked GlcNAc which can occupy the anchor site. It has been proposed that the conformation of the catalytic site depends on the presence of a GlcNAc residue in the anchoring site. | Defined by 5 residues: HIS:A-90ASP:A-92ASP:A-204ASP:A-341HIS:A-471 | EC: 3.2.1.114 (PDB Primary Data) |