› 2vjv

X-ray diffraction
1.9Å resolution

Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site

Released:
DOI: 10.2210/pdb2vjv/pdb
PDB entry 2vjv coloured by chain, front view.
PDB entry 2vjv coloured by chain, side view.
PDB entry 2vjv coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection.
Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F
Cell 132 208-20 (2008)
PMID: 18243097

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115879 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transposase IS200-like domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 159 amino acids
Theoretical weight: 18.39 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q933Z0 (Residues: 2-155; Coverage: 99%)
Gene names: B0X28_06285, B0X28_06415, B0X28_06965, B0X28_07035, B0X28_07355, B0X28_07380, B0X28_07400, B0X28_07410, B0X28_08670, B0X29_00655, B0X39_04170, BB413_07925, BB437_07715, DD756_06260, DDP35_01150, DDP42_08030, EC527_06560, EC565_08270, EPC71_00690, EPC72_02395, tnpA
Sequence domains: Transposase IS200 like
Structure domains: Transposase IS200-like
5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 26 nucleotides
Theoretical weight: 8 KDa
Source organism: Helicobacter pylori
Expression system: Not provided
5'-D(*DT*DA*DT*DT*DA*DCP)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: Helicobacter pylori
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 66.292Å b: 72.407Å c: 110.174Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

16 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
15 more

6 mentions without citation

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily.
Chandler et al. (2013)
5 more