1X9D

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1x9da_	All alpha proteins	alpha/alpha toroid	Seven-hairpin glycosidases	Class I alpha-1	2-mannosidase, catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class I alpha-1, 2-mannosidase, catalytic domain	8021274	4001178	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Seven-hairpin glycosidases	8033654	3000996	SCOP2 (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	Glyco_hydro_47	e1x9dA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Glyco_hydro_47	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.50.10.10	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01532	Glycosyl hydrolase family 47 (Glyco_hydro_47)	Glycosyl hydrolase family 47	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding mannosyl-oligosaccharide mannosidase activity hydrolase activity, acting on glycosyl bonds mannosyl-oligosaccharide 1,2-alpha-mannosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity alpha-mannosidase activity catalytic activity	carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process mannoprotein catabolic process proteolysis involved in protein catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process mannoprotein metabolic process proteolysis metabolic process protein metabolic process carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process mannoprotein catabolic process proteolysis involved in protein catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process mannoprotein metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process carbohydrate derivative biosynthetic process cellular biosynthetic process cellular metabolic process glycoprotein biosynthetic process protein glycosylation macromolecule biosynthetic process biosynthetic process glycosylation macromolecule modification macromolecule glycosylation cellular process protein modification process carbohydrate metabolic process oligosaccharide metabolic process cellular response to stimulus response to stimulus response to nitrogen compound proteasomal protein catabolic process ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress viral gene expression viral protein processing viral process protein alpha-1,2-demannosylation protein deglycosylation protein demannosylation	membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle endoplasmic reticulum endoplasmic reticulum quality control compartment endomembrane system membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle endoplasmic reticulum endoplasmic reticulum quality control compartment endomembrane system membrane Golgi apparatus extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050749	Glycosyl Hydrolase Family 47	Family
A	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A	IPR036026	Seven-hairpin glycosidases	Homologous Superfamily
A	IPR001382	Glycoside hydrolase family 47	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UKM7	intellectual disability Rafiq syndrome congenital disorder of glycosylation Mental Retardation, Psychosocial non-syndromic intellectual disability ovarian cancer

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	mannosyl-oligosaccharide 1,2-alpha-mannosidase M-CSA #19	Class I alpha-1,2-mannosidases are conserved throughout eukaryotic evolution and are members of the glycoside hydrolase family 47. They regulate the maturation of N-glycans during glycoprotein biosynthesis. N-glycan formation begins with the transfer of a preformed oligosaccharide precursor, usually Glc3Man9ClcNac2, to nascent polypeptide chains. The oligosaccharide precursor is then trimmed immediately by alpha-glucosidases and alpha-mannosidases in the endoplasmic reticulum or the golgi apparatus. Besides their importance in N-glycan maturation, endoplasmic reticulum and golgi apparatus processing glycosidases and mannosidases also play a role in protein folding \"quality control\". Trimming of mannose residues in the endoplasmic reticulum acts as a signal to target misfolded glycoproteins for degradation by the proteasome, which ensures only correctly folded proteins are transported to their final destination. Mannosyl-oligosaccharide 1,2-alpha-mannosidase is the only alpha-mannosidase in Saccharomyces cerevisae and it removes a single mannose residue from Man(9)(GlcNAc)(2) to form Man(8)(GlcNAc)(2) in the endoplasmic reticulum as do equivalent enzymes in higher organisms. Class I enzymes found in the golgi apparatus remove all four linked alpha-mannose residues.	Defined by 4 residues: GLU:A-169 [auth A-330]ARG:A-173 [auth A-334]ASP:A-302 [auth A-463]GLU:A-438 [auth A-599] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.1.113 (PDB Primary Data) Search M-CSA Motif + EC 3.2.1.113

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.