› 6ter

X-ray diffraction
1.68Å resolution

Crystal structure of a galactokinase from Bifidobacterium infantis in complex with Galactose

Released:
DOI: 10.2210/pdb6ter/pdb
PDB entry 6ter coloured by chain, front view.
PDB entry 6ter coloured by chain, side view.
PDB entry 6ter coloured by chain, top view.
Source organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Primary publication:
Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-fluorinated Monosaccharides.
Keenan T, Parmeggiani F, Malassis J, Fontenelle CQ, Vendeville JB, Offen W, Both P, Huang K, Marchesi A, Heyam A, Young C, Charnock SJ, Davies GJ, Linclau B, Flitsch SL, Fascione MA
Cell Chem Biol 27 1199-1206.e5 (2020)
PMID: 32619452

Function and Biology Details

Reaction catalysed: 
ATP + alpha-D-galactose = ADP + alpha-D-galactose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110477 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
galactokinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 429 amino acids
Theoretical weight: 45.82 KDa
Source organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B7GUI0 (Residues: 1-416; Coverage: 100%)
Gene name: Blon_2062
Sequence domains:

Ligands and Environments

9 bound ligands:
Ligand GOL 27 x GOL
Ligand PEG 26 x PEG
Ligand PGE 4 x PGE
Ligand PG4 2 x PG4
Ligand GLA 4 x GLA
Ligand GAL 2 x GAL
Ligand CL 3 x CL
Ligand NA 6 x NA
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 52.32Å b: 164.929Å c: 113.63Å
α: 90° β: 94.97° γ: 90°
R-values:
R R work R free
0.228 0.224 0.308
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Biocatalytic Approaches to Building Blocks for Enzymatic and Chemical Glycan Synthesis.
Dolan et al. (2023)
6 other articles