Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes

Proc Natl Acad Sci U S A. 1986 Oct;83(20):7648-52. doi: 10.1073/pnas.83.20.7648.


A computer analysis of the amino acid sequences from the putative gene products of retroviral pol genes has revealed a 150-residue segment that is homologous with the ribonuclease H of Escherichia coli. The segment occurs at the carboxyl terminus of the region assigned to the 90-kDa reverse transcriptase polypeptide. In contrast, a section nearer the amino terminus of this sequence can be aligned with nonretroviral polymerases. The order of activities in the pol gene is thus: polymerase-ribonuclease-endonuclease. On another note, all retroviral endonuclease sequences contain a consensus zinc-binding "finger." This should not be confused with the well-known zinc requirement of reverse transcriptases.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Computers
  • DNA Helicases / analysis*
  • Endoribonucleases / analysis*
  • Genes, Viral*
  • Integrases
  • RNA-Directed DNA Polymerase / analysis*
  • Retroviridae / enzymology*
  • Retroviridae / genetics
  • Ribonuclease H
  • Viral Proteins / analysis*


  • Viral Proteins
  • Integrases
  • RNA-Directed DNA Polymerase
  • Endoribonucleases
  • Ribonuclease H
  • DNA Helicases