› 1u8b

X-ray diffraction
2.1Å resolution

Crystal structure of the methylated N-ADA/DNA complex

Released:
DOI: 10.2210/pdb1u8b/pdb
PDB entry 1u8b coloured by chain, front view.
PDB entry 1u8b coloured by chain, side view.
PDB entry 1u8b coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada.
He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dötsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL
Mol Cell 20 117-29 (2005)
PMID: 16209950

Function and Biology Details

Reactions catalysed: 
DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
DNA (containing Sp-methylphosphotriester) + protein L-cysteine = DNA (without Sp-methylphosphotriester) + protein S-methyl-L-cysteine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114689 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Bifunctional transcriptional activator/DNA repair enzyme Ada Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P06134 (Residues: 8-139; Coverage: 37%)
Gene names: JW2201, ada, b2213
Sequence domains:
Structure domains:
5'-D(*TP*AP*AP*AP*TP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(P*AP*AP*TP*TP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.49 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3' Chain: E
Molecule details ›
Chain: E
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
2 modified residues:
Ligand MSE 3 x MSE
Ligand SMC 1 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 28.842Å b: 84.593Å c: 108.357Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.235 0.274
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

17 review citations

Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation.
Shrivastav et al. (2010)
16 more

3 mentions without citation

High performance transcription factor-DNA docking with GPU computing.
Wu et al. (2012)
2 more