› 1y6f

X-ray diffraction
2.4Å resolution

alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site

Released:
DOI: 10.2210/pdb1y6f/pdb
PDB entry 1y6f coloured by chain, front view.
PDB entry 1y6f coloured by chain, side view.
PDB entry 1y6f coloured by chain, top view.
Source organism: Tequatrovirus T4
Primary publication:
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.
Larivière L, Sommer N, Moréra S
J Mol Biol 352 139-50 (2005)
PMID: 16081100

Function and Biology Details

Reaction catalysed: 
Transfers an alpha-D-glucosyl residue from UDP-glucose to a hydroxymethylcytosine residue in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218909 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA alpha-glucosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 403 amino acids
Theoretical weight: 47.04 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04519 (Residues: 1-400; Coverage: 100%)
Gene name: agt
Sequence domains: DNA alpha-glucosyltransferase
Structure domains: Glycogen Phosphorylase B;
5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.89 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand UPG 1 x UPG
Ligand GOL 4 x GOL
Ligand PEG 2 x PEG
Ligand UDP 1 x UDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 47.363Å b: 123.964Å c: 86.628Å
α: 90° β: 101.83° γ: 90°
R-values:
R R work R free
0.197 0.197 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Glycosyltransferases: structures, functions, and mechanisms.
Lairson et al. (2008)
1 more

4 mentions without citation

Extrahelical damaged base recognition by DNA glycosylase enzymes.
Stivers JT. (2008)
3 more