› 6gvd

X-ray diffraction
1.22Å resolution

Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose

Released:
DOI: 10.2210/pdb6gvd/pdb
PDB entry 6gvd coloured by chain, front view.
PDB entry 6gvd coloured by chain, side view.
PDB entry 6gvd coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Primary publication:
Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Ren W, Pengelly R, Farren-Dai M, Shamsi Kazem Abadi S, Oehler V, Akintola O, Draper J, Meanwell M, Chakladar S, Świderek K, Moliner V, Britton R, Gloster TM, Bennet AJ
Nat Commun 9 3243 (2018)
PMID: 30104598

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 MSB8
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
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 2 x SO4
Ligand MG 3 x MG
Ligand FDK 1 x FDK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 66.957Å b: 96.135Å c: 97.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.151 0.149 0.188
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

10 citation in other articles

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.
Wilson et al. (2021)
9 more

1 mention without citation

Structural insight into the hydrolase and synthase activities of an alkaline α-galactosidase from Arabidopsis from complexes with substrate/product.
Chuankhayan et al. (2023)