› 1dl2

X-ray diffraction
1.54Å resolution

CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACCHAROMYCES CEREVISIAE AT 1.54 ANGSTROM RESOLUTION

Released:
DOI: 10.2210/pdb1dl2/pdb
PDB entry 1dl2 coloured by chain, front view.
PDB entry 1dl2 coloured by chain, side view.
PDB entry 1dl2 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.
Vallée F, Lipari F, Yip P, Sleno B, Herscovics A, Howell PL
EMBO J 19 581-8 (2000)
PMID: 10675327

Function and Biology Details

Reaction catalysed: 
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152495 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase Chain: A
Molecule details ›
Chain: A
Length: 511 amino acids
Theoretical weight: 58.77 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P32906 (Residues: 34-549; Coverage: 93%)
Gene names: J2110, MNS1, YJR131W
Sequence domains: Glycosyl hydrolase family 47
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, NDG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand CA 1 x CA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: P3121
Unit cell:
a: 88.397Å b: 88.397Å c: 153.22Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.209 0.227
Expression system: Komagataella pastoris

Quick links

Citations

14 review citations

Roles of N-linked glycans in the endoplasmic reticulum.
Helenius et al. (2004)
13 more

9 mentions without citation

Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.
Vallée et al. (2000)
8 more