DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTLDRHGH 42
Cdd:cd01189   108 PHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYAH 147

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTLDRHGH 42
Cdd:cd01189   108 PHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYAH 147

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2566640626   1 MVPHGLGHTTASLAISAGANVKVVQRLLGHAAAAMT 36
Cdd:pfam00589 126 LHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT 161

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTLDRHGH 42
Cdd:cd01189   108 PHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYAH 147

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTLDRHGHLLNDD 47
Cdd:cd01186   136 PHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLNTYGHLSEED 180

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTL 37
Cdd:cd00397   130 PHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2566640626   1 MVPHGLGHTTASLAISAGANVKVVQRLLGHAAAAMTlDRHGH 42
Cdd:cd00796   122 LRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMT-MRYAH 162

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.

                          10        20
                  ....*....|....*....|....*....
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHA 31
Cdd:cd00798   128 PHTLRHSFATHLLEGGADLRVVQELLGHA 156

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2566640626   1 MVPHGLGHTTASLAISAGANVKVVQRLLGHAAAAMT 36
Cdd:COG0582   325 FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKV 360

tyrosine recombinase;

                          10        20
                  ....*....|....*....|....*....
gi 2566640626   3 PHGLGHTTASLAISAGANVKVVQRLLGHA 31
Cdd:PRK00283  244 PHVLRHAFATHLLNHGADLRVVQELLGHS 272