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 1266711286 392 LLAVDIFTTTGARLNELLQLNSEkdclraikvngDLKFSFYAI-----PKGRDKPESYPISKQTFQLIKRvnlMLKEHYN 466
Cdd:cd00397    20 RAILLLLLETGLRISELLALKVK-----------DIDLDNGTIrvrgkKTKGGKERTVPLPKELAEELKE---YLKERRD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1266711286 467 GTIPsvtYRGERKHLFPEPKPYFFQYNEKALNRHSVTACLRFLLHglffetqegetvvIKTHLLRHAFATEAVqRQEIPI 546
Cdd:cd00397    86 KRGP---LLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK-------------ITPHSLRHTFATNLL-ENGVDI 148

                         170
                  ....*....|....*...
gi 1266711286 547 DIVAKMLHQHDLNVTRYY 564
Cdd:cd00397   149 KVVQKLLGHSSISTTQRY 166

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 1266711286 392 LLAVDIFTTTGARLNELLQLNSEkdclraikvngDLKFSFYAI-----PKGRDKPESYPISKQTFQLIKRvnlMLKEHYN 466
Cdd:cd00397    20 RAILLLLLETGLRISELLALKVK-----------DIDLDNGTIrvrgkKTKGGKERTVPLPKELAEELKE---YLKERRD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1266711286 467 GTIPsvtYRGERKHLFPEPKPYFFQYNEKALNRHSVTACLRFLLHglffetqegetvvIKTHLLRHAFATEAVqRQEIPI 546
Cdd:cd00397    86 KRGP---LLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK-------------ITPHSLRHTFATNLL-ENGVDI 148

                         170
                  ....*....|....*...
gi 1266711286 547 DIVAKMLHQHDLNVTRYY 564
Cdd:cd00397   149 KVVQKLLGHSSISTTQRY 166

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 1266711286 392 LLAVDIFTTTGARLNELLQLNSEkdclraikvngDLKFSFYAI-----PKGRDKPESYPISKQTFQLIKRvnlMLKEHYN 466
Cdd:cd00397    20 RAILLLLLETGLRISELLALKVK-----------DIDLDNGTIrvrgkKTKGGKERTVPLPKELAEELKE---YLKERRD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1266711286 467 GTIPsvtYRGERKHLFPEPKPYFFQYNEKALNRHSVTACLRFLLHglffetqegetvvIKTHLLRHAFATEAVqRQEIPI 546
Cdd:cd00397    86 KRGP---LLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK-------------ITPHSLRHTFATNLL-ENGVDI 148

                         170
                  ....*....|....*...
gi 1266711286 547 DIVAKMLHQHDLNVTRYY 564
Cdd:cd00397   149 KVVQKLLGHSSISTTQRY 166

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1266711286 400 TTGARLNELLQLnsekdclRAIKVNGDLKFSFYAIPKGRdKPESYPISKQTFQLIKRvnlmLKEHYNGTIPSVTYRgerk 479
Cdd:cd00796    34 YTGARRGEILSL-------RWDDIDLEVGLIVLPETKNG-KPRTVPLSDEAIAILKE----LKRKRGKDGFFVDGR---- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1266711286 480 hlfpepkpyFFQYNEKALNRHSVTACLRFLLHGLffetqegetvviKTHLLRHAFATEAVQRQeIPIDIVAKML-HQhDL 558
Cdd:cd00796    98 ---------FFGIPIASLRRAFKKARKRAGLEDL------------RFHDLRHTFASRLVQAG-VPIKTVAKILgHS-SI 154

                  ....*.
gi 1266711286 559 NVTRYY 564
Cdd:cd00796   155 KMTMRY 160