The 'helix clamp' in HIV-1 reverse transcriptase: a new nucleic acid binding motif common in nucleic acid polymerases

Nucleic Acids Res. 1994 Nov 11;22(22):4625-33. doi: 10.1093/nar/22.22.4625.


Amino acid sequences homologous to 259KLVGKL (X)16KLLR284 of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) are conserved in several nucleotide polymerizing enzymes. This amino acid motif has been identified in the crystal structure model as an element of the enzyme's nucleic acid binding apparatus. It is part of the helix-turn-helix structure, alpha H-turn-alpha I, within the 'thumb' region of HIV-1 RT. The motif grasps the complexed nucleic acid at one side. Molecular modeling studies on HIV-1 RT in complex with a nucleic acid fragment suggest that the motif has binding function in the p66 subunit as well as in the p51 subunit, acting as a kind of 'helix clamp'. Given its wide distribution within the nucleic acid polymerases, the helix clamp motif is assumed to be a structure of general significance for nucleic acid binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Computer Simulation
  • DNA / metabolism
  • Databases, Factual
  • HIV Reverse Transcriptase
  • HIV-1 / enzymology*
  • Helix-Loop-Helix Motifs / genetics*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleotidyltransferases / chemistry*
  • Nucleotidyltransferases / genetics
  • Nucleotidyltransferases / metabolism
  • Protein Structure, Secondary*
  • RNA / metabolism
  • RNA-Directed DNA Polymerase / chemistry*
  • RNA-Directed DNA Polymerase / genetics
  • RNA-Directed DNA Polymerase / metabolism
  • Sequence Homology, Amino Acid


  • RNA primers
  • RNA
  • DNA
  • Nucleotidyltransferases
  • HIV Reverse Transcriptase
  • RNA-Directed DNA Polymerase