{PDOC00334} {PS00397; RECOMBINASES_1} {PS00398; RECOMBINASES_2} {PS51736; RECOMBINASES_3} {BEGIN} ********************************************************************* * 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 gamma-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 AlphaBeta fold and consists of a five-stranded mixed beta-sheet surrounded by three alpha helices on one side and one helix on the other (see ) [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. -Consensus pattern: Y-[LIVAC]-R-[VA]-S-[ST]-x(2)-Q [S is the active site residue] -Sequences known to belong to this class detected by the pattern: ALL, except for Uvp1 which has Lys instead of Val in position 4 of the pattern. -Other sequence(s) detected in Swiss-Prot: a hypothetical protein from phage Phi-105 which contains only 82 amino acids, but whose N-terminal section is surprisingly similar to that of resolvases and 3 other proteins. -Consensus pattern: G-[DE]-x(2)-[LIVM]-{E}-x-{V}-[LIVM]-[DT]-R-[LIVM]-[GSA] -Sequences known to belong to this class detected by the pattern: ALL, except for Tn1546 resolvase and cisA. -Other sequence(s) detected in Swiss-Prot: 4. -Sequences known to belong to this class detected by the profile: ALL. -Other sequence(s) detected in Swiss-Prot: NONE. -Last update: October 2014 / Profile added and text revised. [ 1] Argos 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 "The integrase family of site-specific recombinases: regional similarities and global diversity." EMBO J. 5:433-440(1986). PubMed=3011407 [ 2] Garnier T., Saurin W., Cole S.T. "Molecular characterization of the resolvase gene, res, carried by a multicopy plasmid from Clostridium perfringens: common evolutionary origin for prokaryotic site-specific recombinases." Mol. Microbiol. 1:371-376(1987). PubMed=2896291 [ 3] Sato T., Samori Y., Kobayashi Y. "The cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologous to a site-specific recombinase." J. Bacteriol. 172:1092-1098(1990). PubMed=2105293 [ 4] Gigliani F., Sporeno E., Perri S., Battaglia P.A. "The uvp1 gene of plasmid pR cooperates with mucAB genes in the DNA repair process." Mol. Gen. Genet. 218:18-24(1989). PubMed=2550763 [ 5] Yang W., Steitz T.A. "Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site." Cell 82:193-207(1995). PubMed=7628011 -------------------------------------------------------------------------------- PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html -------------------------------------------------------------------------------- {END}