PROSITE documentation PDOC00334

Site-specific recombinase catalytic domain signatures and profile

Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur:

• Recombination between inverted repeats resulting in the reversal of a DNA segment.
• Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment.

Site-specific recombination is characterized by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation.

Two unrelated families of recombinases are currently known [1]. The first, called the tyrosine recombinases or lambda integrase family, groups a number of bacterial, phage and yeast plasmid enzymes. The second [2], called the serine recombinases or resolvase/invertase family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA, and a C-terminal helix-turn-helix DNA-binding domain.

The resolvase/invertase family is currently known to include the following proteins:

• DNA invertase from Salmonella typhimurium (gene hin). Hin can invert a 900 bp DNA fragment adjacent to a gene for one of the flagellar antigens.
• DNA invertase from Escherichia coli (gene pin).
• DNA invertase from Bacteriophage Mu (gene gin), P1 and P7 (gene cin).
• Resolvases from transposons Tn3, Tn21, Tn501, Tn552, Tn917, Tn1546, Tn1721, Tn2501 and Tn1000 (known as γ-delta resolvase).
• Resolvase from Clostridium perfringens plasmid pIP404.
• Resolvase from Escherichia coli plasmid R46.
• Resolvase from Escherichia coli plasmid RP4 (gene parA).
• A putative recombinase from Bacillus subtilis (gene cisA) [3] which plays an important role in sporulation by catalyzing the recombination of genes spoIIIC and spoIVCB to form polymerase sigma-K factor.
• Uvp1, a protein from Escherichia coli plasmid pR which cooperates with the mucAB genes in the DNA repair process and could be a resolvase [4].

Generally, proteins from the resolvase family have 180 to 200 amino-acid residues, excepting cisA which is much larger (500 residues).

The N-terminal resolvase/invertase-type recombinase catalytic domain has an αβ fold and consists of a five-stranded mixed β-sheet surrounded by three α helices on one side and one helix on the other (see <PDB:1GDT>) [5].

We developed two signature patterns for the resolvase family. The first is based on a highly conserved region in the N-terminal extremity of these proteins; it contains a serine residue most probably involved in covalent attachment to DNA. The second pattern is based on a conserved region located about 50 residues upstream of the serine active site. We also developed a profile which covers the entire resolvase/invertase-type recombinase catalytic domain.