PROSITE documentation PDOC50879
Ribonuclease (RNase) H type-I and type-2 domains profiles


Ribonuclease H (RNase H) (EC, one member of the ribonuclease family, recognizes and cleaves the RNA strand of RNA-DNA heteroduplexes. The enzyme is widely present in all three kingdoms of living organisms, including bacteria, archaea, and eukaryotes, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements. RNases H are classified into two evolutionarily unrelated families, type-I and type-II RNase H, with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. There appears to be three evolutionarily distinct lineages of cellular Rnase H enzymes. Type-I or RNase HI domains have been found in all Eukarya, one Archaea, many Eubacteria, a few non-LTR retroposons and all LTR retrotransposons. Type II enzymes consist of RNase HII (rnhB) and HIII (rnhC), which are homologous enzymes. RNase HII can be found in Archaea, Eubacteria and all Eukarya, while RNase HIII appears only in some Eubacteria. In eukaryotes and all Archaea, RNase HII enzymes may constitute the bulk of all RNH activity, while the reverse is true in Eubacteria like E. coli where RNase HI is the major source of RNH activity. All LTR retrotransposons acquired an enzymatically weak RNase H domain that is missing an important catalytic residue found in all other RNase H enzymes. Vertebrate retroviruses appear to have reacquired their RNase H domains, which are catalytically more active, but their ancestral RNase H domains (found in other LTR retrotransposons) have degenerated to give rise to the tether domain unique to vertebrate retrovirus [1,2,3,4].

The main element of the RNase H-like catalytic core is a β-sheet comprising five β-strands, ordered 3-2-1-4-5, where the β-strand 2 is antiparallel to the other β-strands. On both sides the central β-sheet is flanked by α-helices, the number of which differs between related enzymes. The catalytic residues for RNase H enzymatic activity (three aspartic acid and one glutamic acid residue) are invariant across all RNase H domains [1,4].

The profiles we developed cover the whole RNase H type-1 and type-2 domains.

Last update:

May 2021 / Text revised; profiles added.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

RNASE_H_1, PS50879; RNase H type-1 domain profile  (MATRIX)

RNASE_H_2, PS51975; Ribonuclease (RNase) H type-2 domain profile  (MATRIX)


1AuthorsHyjek M. Figiel M. Nowotny M.
TitleRNases H: Structure and mechanism.
SourceDNA Repair. (Amst). 84:102672-102672(2019).
PubMed ID31371183

2AuthorsKochiwa H. Tomita M. Kanai A.
TitleEvolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.
SourceBMC Evol. Biol. 7:128-128(2007).
PubMed ID17663799

3AuthorsMalik H.S.
TitleRibonuclease H evolution in retrotransposable elements.
SourceCytogenet. Genome Res 110:392-401(2005).
PubMed ID16093691

4AuthorsChon H. Matsumura H. Koga Y. Takano K. Kanaya S.
TitleCrystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus.
SourceJ. Mol. Biol. 356:165-178(2006).
PubMed ID16343535

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