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- *****************************************
- * Site-specific recombinases signatures *
- *****************************************
-
- 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 `phage integrase' family, groups a number of bacterial, phage and
- yeast plasmid enzymes. The second [2], called the `resolvase' 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 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).
-
- 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.
-
- -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 a mosquito trypsinogen-like
- protease.
-
- -Consensus pattern: G-[DE]-x(2)-[LIVM]-x(3)-[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: fission yeast 4-nitrophenyl-
- phosphatase.
-
- -Last update: June 1994 / Text revised.
-
- [ 1] Argos P., Landy A., Abremski K., Egan J.B., Haggard-Ljungquist E.,
- Hoess R.H., Kahn M.L., Kalionis B., Narayama S., Pierson L.S. III,
- Sternberg N., Leong J.M.
- EMBO J. 5:433-440(1986).
- [ 2] Garnier T., Saurin W., Cole S.T.
- Mol. Microbiol. 1:371-376(1987).
- [ 3] Sato T., Samori Y., Kobayashi Y.
- J. Bacteriol. 172:1092-1098(1990).
- [ 4] Gigliani F., Sporeno E., Perri S., Battaglia P.A.
- Mol. Gen. Genet. 218:18-24(1989).
-