InterPro domain: IPR012337

The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3'-5' exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [ 1 , 2 , 3 ].

This superfamily also includes the YqgF domain, described as RNase H-like and typified by the Escherichia coli protein YqgF [ 4 , 5 ]. YqgF domain-containing proteins are predicted to be ribonucleases or resolvases based on homology to RuvC Holliday junction resolvases.

1. Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form. Acta Crystallogr. D Biol. Crystallogr. 49, 423-7
2. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6, 76-83
3. Functional dissection of the Schizosaccharomyces pombe Holliday junction resolvase Ydc2: in vivo role in mitochondrial DNA maintenance. Eur. J. Biochem. 270, 2837-47
4. Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold. J. Biomol. NMR 27, 389-92
5. SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28, 3417-32