Protein Name

Integron integrase-attC sequence complex


Vibria cholelae

Biological Context

Bacteria have been exchanging the genetic information among the different species during the evolution. This type of trans-gene movement is called “lateral DNA transfer”. Transfer of drug resistance genes and toxic substance encoding genes is essential for their survival. DNA recombination with recombinase is the one of the most important event when lateral DNA transfer occurs. The protein described here is a recombinase, Integron integrase(IntI). IntI conducts the DNA recombination by cutting and inserting a special DNA sequence, integron. IntI mediated DNA recombination starts from the insertion of the donor DNA between two insertion sequences, attI and attC in the integron. Surprisingly, the attC site shows poor sequence conservation while the attI site is conserved among species. Therefore, it has been suggested that a sequence independent recognition mechanism of attC site may exist.

Structure Description


V.chleae Integron integraseA (VchIntIA) and attC site(V.cholelae repeat sequence: VCR sequence) complex is described here. The VchIntIA-VCR complex contains four VchIntIA molecules bound to two antiparallel VCR duplexes. There are two kinds of VchIntIAs in the complex despite each of them has the same amino acid sequence; one is the attacking subunit which cleaves DNA with a tyrosine residue(Y302), and the other is non-attacking subunit which does not cleave DNA (Fig.1). Single-stranded DNA of VCR sequence folds into duplex, however T12 and G20 do not have complementary bases and are exposed to the extrahelical region. These two bases are the important for VchIntIA to recognize the attC site and to form the dyad synaptic assembly of the complex. T12 interacts with H240, H241 and P232 near the beta-4,5 hairpin of non-attacking subunit, which mainly contributes to the attC site recognition of VchIntIA. On the other hand, G20 interacts with W157 and W219 of attacking subunit across the synaptic interface, which holds the synapse together. Additionally, the reminder of protein-DNA interface is composed almost entirely of non-specific phosphate interaction. These interactions suggest that the attC site recognition of IntIs does not require the specific sequence but depends on the position of two flipped bases.


Fig. 1 VchIntIA-VCR sequence complex; red: attacking subunit, green: non-attacking subunit, orange: VCR sequence

Protein Data Bank (PDB)



MacDonald, D. Demarre, G. Bouvier, M. Mazel, D. Gopaul, D.N.; "Structural basis for broad DNA-specificity in integron recombination"; Nature; (2006) 440:1157-1162.


author: Daisuke Ino

Japanese version:PDB:2A3V