Gamma delta resolvase / DNA complex
Human genome composed of approximately 3.2*10 to the power of 9 nucleotides (two meters long, if stretched) in each cell. The striking feature of the human genome is that only a minor fraction of the genomic DNA (only 1.5 %) encodes structural proteins or and structural and catalytic RNAs. Much of the remaining chromosomal DNA (about 50 %) is made up of short mobile pieces of DNA called transposable elements, that have gradually accumulated in the chromosome over evolutionary time. The transposable elements are transferred by site-specific recombination between two different positions in a single chromosome or between two different chromosomes. The size of the transposable elements ranges from a few hundred to ten thousands of nucleotide pairs. Viruses (e.g., HIV) use this site-specific recombination to transfer their genomes into host DNA, and bacteria also use this mechanism for their activities. In transposition, a specific enzyme called transposase, usually encoded by the transposon, acts on a specific DNA sequence at each end of the transposable element (mark for transposase); first disconnecting it from the DNA and then inserting it into a new target DNA site. The mechanism of this cut-and-paste transposition by transposase is still under study.
The structure shown here is a complex of a kind of transposase, delta gamma resolvase of Escherichia coli, with 34 bp DNA fragment, which is a mark sequence for resolvase to bind. Delta gamma resolvase forms a homodimer in solution and converts a negatively supercoiled circular DNA containing mark sequence called res, into two catenated molecules via double-strand DNA cleavage, strand exchange, and religation. In this structure, delta gamma resolvase forms dimer, and a DNA fragment fits between them. Each subunit has an alpha beta fold N-terminal catalytic domain, a 3-helix-bundle C terminal DNA-binding domain, and an extended arm region that connects the two domains and binds DNA around the minor groove. The DNA fragment is sharply kinked at it center, giving rise to an overall bend of 60 degree toward the major groove. This structure postulates that the DNA becomes partially denatured around the crossover point following the cleavage and religation.
Protein Data Bank (PDB)
author: Sachiyo Nomura