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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757757540  45 TGGGYSVRGARGLTQWAIAQLLEvmsdltepeRRKLA-----STSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTS 119
Cdd:cd01196   99 TRGGTRKLTHNPLTQANAYRMVR---------RRAIAadiptAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQ 169

                 ..
gi 757757540 120 IY 121
Cdd:cd01196  170 LY 171

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 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYV 122
Cdd:cd00397  129 TPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167

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 757757540   84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYV 122
Cdd:pfam00589 127 HPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYT 165

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757757540  45 TGGGYSVRGARGLTQWAIAQLLEvmsdltepeRRKLA-----STSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTS 119
Cdd:cd01196   99 TRGGTRKLTHNPLTQANAYRMVR---------RRAIAadiptAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQ 169

                 ..
gi 757757540 120 IY 121
Cdd:cd01196  170 LY 171

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 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYV 122
Cdd:cd00397  129 TPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 757757540  76 ERRKLASTSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTT-SIYVSPEEARMRRE 132
Cdd:cd01186  127 KKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlNTYGHLSEEDIRRE 184

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 757757540  57 LTQWAIAQLLE--VMSDLTEpeRRKLASTSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTT-SIYV 122
Cdd:cd01189   80 LPDELIELLKElkAFKKLLK--KAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTlDVYA 146

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        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 757757540  52 RGARgLTQWAIAQLLE---VMSDLTEPerrklasTSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIY--VSPE 125
Cdd:cd00798  100 RGKR-LSRRGVWRILKkyaERAGLPKH-------VSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYthVSFE 170

Site-specific recombinase XerC [Replication, recombination and repair];

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYV 122
Cdd:COG4973  237 HPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYT 275

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIY 121
Cdd:cd01193  136 TPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173

tyrosine recombinase;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYVSPEEARMRREAAKYHAR 139
Cdd:PRK00283 243 SPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPR 298

site-specific tyrosine recombinase XerC; Reviewed

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 757757540  86 HAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIY 121
Cdd:PRK01287 268 HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303

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 757757540  76 ERRKLASTSPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIYV 122
Cdd:cd00796  115 KRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYA 161

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing 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
                 ....*....|....*....|....*....|....
gi 757757540  86 HAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTS 119
Cdd:cd01184  142 HSFRHTFITALKRAGVPEELIAQIVGHSRGGVTH 175

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLG-TTSIY-VSPEEARMRREAAKYHARL 140
Cdd:cd00801  122 TPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGvVRAAYnRYDYLEERREALQAWADYL 180

integron integrase;

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 757757540  84 SPHAFRHTVGTQMLAAGVALEVVQRTLGHASLGTTSIY 121
Cdd:PRK15417 275 TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312