PROSITE documentation PDOC50878
Reverse transcriptase (RT) catalytic domain profile


Retroviral reverse transcriptases (EC (prototypical RTs) exhibit three enzymatic activities: an RNA-dependent DNA polymerase, Ribonuclease H, and a DNA-dependent DNA polymerase. These are employed in copying the plus strand RNA genome to produce a minus strand of DNA, removal of the RNA template, and synthesis of the plus strand of DNA using the minus-strand DNA as a template, respectively [1]. Both polymerase activities are performed by the RT domain whereas the ribonuclease activity is achieved by the RNase H domain (see <PDOC50879>).

Several crystal structures of the RT domain have been determined (see for example <PDB:3HVT>) [2]. Structurally, the RT domain can be divided in four subdomains. Its anatomical resemblance to a right hand has led to naming the subdomains as fingers, palm, and thumb. The fourth subdomain lies between the rest of the RT and the RNase H domain leading it to be called the connection subdomain. The palm domain contains the catalytic triad critical for polymerase activity, and its folded structure resembles that of the corresponding catalytic domain in other DNA and RNA polymerases. The position of fingers and thumb defined a deep cleft, with polymerase active residues at its base.

Proteins known to contain an RT domain are listed below:

  • Retroviral reverse transcriptase.
  • Catalytic subunit of the telomerase.
  • Eukaryotic retrotransposons.
  • Escherichia coli retroelement retron, which is responsible for the synthesis of multicopy single-stranded DNA (msDNA).
  • Bacterial mobile group II intron, that can reverse splice into DNA target substrate.

The finger, thumb and connection subdomains are less conserved among all RT domain subfamilies [3] and could not be identified by the profile method. The profile we developed is thus directed against the catalytic region (palm subdomain).

Last update:

October 2004 / First entry.


Technical section

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

RT_POL, PS50878; Reverse transcriptase (RT) catalytic domain profile  (MATRIX)


1AuthorsKatz R.A. Skalka A.M.
TitleThe retroviral enzymes.
SourceAnnu. Rev. Biochem. 63:133-173(1994).
PubMed ID7526778

2AuthorsKohlstaedt L.A. Wang J. Friedman J.M. Rice P.A. Steitz T.A.
TitleCrystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.
SourceScience 256:1783-1790(1992).
PubMed ID1377403

3AuthorsNakamura S.
TitleThe roles of structural imperfections in InGaN-based blue light-emitting diodes and laser diodes .
SourceScience 281:955-961(1998).
PubMed ID9703504

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