› 2ibt

X-ray diffraction
1.7Å resolution

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position

Released:
DOI: 10.2210/pdb2ibt/pdb
PDB entry 2ibt coloured by chain, front view.
PDB entry 2ibt coloured by chain, side view.
PDB entry 2ibt coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence.
Lenz T, Bonnist EY, Pljevaljcić G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E
J Am Chem Soc 129 6240-8 (2007)
PMID: 17455934

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115392 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II methyltransferase M.TaqI Chains: A, D
Molecule details ›
Chains: A, D
Length: 421 amino acids
Theoretical weight: 47.93 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14385 (Residues: 1-421; Coverage: 100%)
Gene name: taqIM
Sequence domains:
Structure domains:
5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
5'-D(*GP*AP*CP*AP*(3DR)P*CP*GP*(6MA)P*AP*C)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 10 nucleotides
Theoretical weight: 2.93 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NEA 2 x NEA
Ligand GOL 7 x GOL
2 modified residues:
Ligand 2PR 2 x 2PR
Ligand 6MA 2 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 59.339Å b: 68.699Å c: 114.022Å
α: 90° β: 92.09° γ: 90°
R-values:
R R work R free
0.169 0.167 0.203
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

2-Aminopurine as a fluorescent probe of DNA conformation and the DNA-enzyme interface.
Jones et al. (2015)
1 more

1 mention without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)