› 1ya6

X-ray diffraction
2.4Å resolution

alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a central A:G mismatch

Released:
DOI: 10.2210/pdb1ya6/pdb
PDB entry 1ya6 coloured by chain, front view.
PDB entry 1ya6 coloured by chain, side view.
PDB entry 1ya6 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-218912 (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(*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NCO 7 x NCO
Ligand UDP 2 x UDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 45.855Å b: 119.318Å c: 86.812Å
α: 90° β: 92.87° γ: 90°
R-values:
R R work R free
0.23 0.23 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

1 mention without citation

Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations.
Yu et al. (2016)