› 5m1i

X-ray diffraction
1.55Å resolution

Structure of GH36 alpha-galactosidase from Thermotoga maritima in a covalent complex with a cyclopropyl carbasugar.

Released:
DOI: 10.2210/pdb5m1i/pdb
PDB entry 5m1i coloured by chain, front view.
PDB entry 5m1i coloured by chain, side view.
PDB entry 5m1i coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.
Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ
Angew Chem Int Ed Engl 55 14978-14982 (2016)
PMID: 27783466

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124427 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-galactosidase Chain: A
Molecule details ›
Chain: A
Length: 575 amino acids
Theoretical weight: 66.2 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli
UniProt:
  • Canonical: G4FEF4 (Residues: 1-552; Coverage: 100%)
Gene names: TM_1192, Tmari_1199, galA
Sequence domains: Melibiase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand 7D8 1 x 7D8
Ligand EDO 12 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 66.903Å b: 96.239Å c: 97.589Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.183
Expression system: Escherichia coli

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Citations

1 review citation

Applications of alkyl orthoesters as valuable substrates in organic transformations, focusing on reaction media.
Khademi et al. (2020)
10 other articles