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.

Last update:

October 2014 / Profile added and text revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

RECOMBINASES_3, PS51736; Resolvase/invertase-type recombinase catalytic domain profile  (MATRIX)

RECOMBINASES_1, PS00397; Site-specific recombinases active site  (PATTERN)

RECOMBINASES_2, PS00398; Site-specific recombinases signature 2  (PATTERN)


1AuthorsArgos P. Landy A. Abremski K. Egan J.B. Haggard-Ljungquist E. Hoess R.H. Kahn M.L. Kalionis B. Narayana S.V. Pierson L.S. III
TitleThe integrase family of site-specific recombinases: regional similarities and global diversity.
SourceEMBO J. 5:433-440(1986).
PubMed ID3011407

2AuthorsGarnier T. Saurin W. Cole S.T.
TitleMolecular characterization of the resolvase gene, res, carried by a multicopy plasmid from Clostridium perfringens: common evolutionary origin for prokaryotic site-specific recombinases.
SourceMol. Microbiol. 1:371-376(1987).
PubMed ID2896291

3AuthorsSato T. Samori Y. Kobayashi Y.
TitleThe cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologous to a site-specific recombinase.
SourceJ. Bacteriol. 172:1092-1098(1990).
PubMed ID2105293

4AuthorsGigliani F. Sporeno E. Perri S. Battaglia P.A.
TitleThe uvp1 gene of plasmid pR cooperates with mucAB genes in the DNA repair process.
SourceMol. Gen. Genet. 218:18-24(1989).
PubMed ID2550763

5AuthorsYang W. Steitz T.A.
TitleCrystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
SourceCell 82:193-207(1995).
PubMed ID7628011

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