InterPro domain: IPR036279

This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include:

• Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins [ 1 ].
• 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [ 2 , 3 ].
• Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases [ 4 ].
• Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair [ 5 ].

1. Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell 85, 1101-12
2. Crystal structure of Thermus aquaticus DNA polymerase. Nature 376, 612-6
3. Structure of taq DNA polymerase shows a new orientation for the structure-specific nuclease domain. Acta Crystallogr. D Biol. Crystallogr. 55, 1971-7
4. Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage. Proc. Natl. Acad. Sci. U.S.A. 96, 38-43
5. The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat. Struct. Biol. 5, 707-13