cd09272

Ty1/Copia family of RNase HI in long-term repeat retroelements

CDD entry
Member databaseCDD
CDD typedomain
Short nameRNase_HI_RT_Ty1
SetRNase_H_like

Description

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms including bacteria, archaea, and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD) are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1, and the vertebrate retroviruses. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
[7, 1, 3, 5, 2, 6, 4]

References

1.Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site. Goedken ER, Marqusee S. J. Biol. Chem. 276, 7266-71, (2001). View articlePMID: 11083878

2.Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W. Mol. Cell 28, 264-76, (2007). View articlePMID: 17964265

3.Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Nowotny M, Yang W. EMBO J. 25, 1924-33, (2006). View articlePMID: 16601679

4.Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Malik HS, Eickbush TH. Genome Res 11, 1187-97, (2001). PMID: 11435400

5.Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. Cell 121, 1005-16, (2005). View articlePMID: 15989951

6.Ribonuclease H. Kanaya S. FEBS J. 276, 1481, (2009). View articlePMID: 19228198

7.Ribonuclease H evolution in retrotransposable elements. Malik HS. Cytogenet Genome Res 110, 392-401, (2005). PMID: 16093691

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