› 5m12

X-ray diffraction
1.53Å resolution

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

Released:
DOI: 10.2210/pdb5m12/pdb
PDB entry 5m12 coloured by chain, front view.
PDB entry 5m12 coloured by chain, side view.
PDB entry 5m12 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
OpenAccess logo 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:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand MG 1 x MG
Ligand 7D0 1 x 7D0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 68.15Å b: 96.04Å c: 98.12Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.222
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)
9 other articles

2 mentions without citation

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Ren et al. (2018)
1 more