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

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- (Hit and III) and exoribonucleases (It, PH and D), Statistical models, hidden Markov models (HMMs), were created for the RNase HII, III, II, 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 sequence alignments for each family suggest amino acids that may be important for their structure, substrate binding and/or catalysis.