{PDOC50878}
{PS50878; RT_POL}
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* Reverse transcriptase (RT) catalytic domain profile *
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Retroviral  reverse  transcriptases (EC 2.7.7.49)   (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).

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: October 2004 / First entry.

[ 1] Katz R.A., Skalka A.M.
     "The retroviral enzymes."
     Annu. Rev. Biochem. 63:133-173(1994).
     PubMed=7526778; DOI=10.1146/annurev.bi.63.070194.001025
[ 2] Kohlstaedt L.A., Wang J., Friedman J.M., Rice P.A., Steitz T.A.
     "Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase
     complexed with an inhibitor."
     Science 256:1783-1790(1992).
     PubMed=1377403
[ 3] Nakamura S.
     "The roles of structural imperfections in InGaN-based blue
     light-emitting diodes and laser diodes ."
     Science 281:955-961(1998).
     PubMed=9703504

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