cd00397

DNA breaking-rejoining enzymes, C-terminal catalytic domain

CDD entry
Member databaseCDD
CDD typedomain
Short nameDNA_BRE_C
SetDNA_BRE_C

Description

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.
[7, 4, 8, 1, 6, 2, 3, 5]

References

1.Structure and mechanism in site-specific recombination. Gopaul DN, Duyne GD. Curr. Opin. Struct. Biol. 9, 14-20, (1999). View articlePMID: 10047575

2.Similarities and differences among 105 members of the Int family of site-specific recombinases. Nunes-Duby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A. Nucleic Acids Res. 26, 391-406, (1998). View articlePMID: 9421491

3.Conserved themes but novel activities in recombinases and topoisomerases. Sherratt DJ, Wigley DB. Cell 93, 149-52, (1998). View articlePMID: 9568707

4.The integrase family of recombinase: organization and function of the active site. Grainge I, Jayaram M. Mol. Microbiol. 33, 449-56, (1999). View articlePMID: 10577069

5.Site-specific recombination in plane view. Yang W, Mizuuchi K. Structure 5, 1401-6, (1997). View articlePMID: 9384556

6.Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. Van Houdt R, Leplae R, Lima-Mendez G, Mergeay M, Toussaint A. Mob DNA 3, 6, (2012). View articlePMID: 22502997

7.Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cheng C, Kussie P, Pavletich N, Shuman S. Cell 92, 841-50, (1998). View articlePMID: 9529259

8.The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Esposito D, Scocca JJ. Nucleic Acids Res. 25, 3605-14, (1997). View articlePMID: 9278480

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