Comparative sequence analysis of ribonucleases HII, III, II PH and D

Nucleic Acids Res. 1997 Aug 15;25(16):3187-95. doi: 10.1093/nar/25.16.3187.


Escherichia coli ribonucleases (RNases) HII, III, II, PH and D have been used to characterise new and known viral, bacterial, archaeal and eucaryotic sequences similar to these endo- (HII and III) and exoribonucleases (II, PH and D). Statistical models, hidden Markov models (HMMs), were created for the RNase HII, III, II and PH and D families as well as a double-stranded RNA binding domain present in RNase III. Results suggest that the RNase D family, which includes Werner syndrome protein and the 100 kDa antigenic component of the human polymyositis scleroderma (PMSCL) autoantigen, is a 3'-->5' exoribonuclease structurally and functionally related to the 3'-->5' exodeoxyribonuclease domain of DNA polymerases. Polynucleotide phosphorylases and the RNase PH family, which includes the 75 kDa PMSCL autoantigen, possess a common domain suggesting similar structures and mechanisms of action for these 3'-->5' phosphorolytic enzymes. Examination of HMM-generated multiple sequences alignments for each family suggest amino acids that may be important for their structure, substrate binding and/or catalysis.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Endoribonucleases / genetics*
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics*
  • Escherichia coli Proteins*
  • Exoribonucleases / genetics*
  • Genes, Bacterial
  • Genes, Fungal
  • Humans
  • Molecular Sequence Data
  • RNA-Binding Proteins / genetics*
  • Ribonuclease H / genetics*
  • Ribonuclease III
  • Sequence Alignment
  • Sequence Analysis


  • Escherichia coli Proteins
  • RNA-Binding Proteins
  • ribonuclease PH
  • Endoribonucleases
  • Exoribonucleases
  • exoribonuclease II
  • ribonuclease HII
  • Ribonuclease III
  • ribonuclease III, E coli
  • Ribonuclease H