› 3lrl

X-ray diffraction
2.4Å resolution

Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae with melibiose

Released:
DOI: 10.2210/pdb3lrl/pdb
PDB entry 3lrl coloured by chain, front view.
PDB entry 3lrl coloured by chain, side view.
PDB entry 3lrl coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases.
Fernández-Leiro R, Pereira-Rodríguez A, Cerdán ME, Becerra M, Sanz-Aparicio J
J Biol Chem 285 28020-33 (2010)
PMID: 20592022

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138199 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Alpha-galactosidase 1 Chain: A
Molecule details ›
Chain: A
Length: 479 amino acids
Theoretical weight: 53.13 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04824 (Residues: 1-471; Coverage: 100%)
Gene name: MEL1
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GLC, GLA
Carbohydrate polymer
2 bound ligands:
Ligand NAG 4 x NAG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P4212
Unit cell:
a: 100.729Å b: 100.729Å c: 111.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.253
Expression system: Saccharomyces cerevisiae

Quick links

Citations

3 review citations

Biotechnological potential of microbial α-galactosidases.
Katrolia et al. (2014)
2 more

1 mention without citation

Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases.
Fernández-Leiro et al. (2010)