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- (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.
Mian
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Sinsheimer Laboratories, University of California Santa Cruz, Santa Cruz, CA 95064, USA. smian@lbl.gov
D000595:Amino Acid Sequence; D004722:Endoribonucleases / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics*; D029968:Escherichia coli Proteins; D005095:Exoribonucleases / Q000235:genetics*; D005798:Genes, Bacterial; D005800:Genes, Fungal; D006801:Humans; D008969:Molecular Sequence Data; D016601:RNA-Binding Proteins / Q000235:genetics*; D016914:Ribonuclease H / Q000235:genetics*; D043244:Ribonuclease III; D016415:Sequence Alignment; D017421:Sequence Analysis
D029968:Escherichia coli Proteins; D016601:RNA-Binding Proteins; C056502:ribonuclease PH; D004722:Endoribonucleases; D005095:Exoribonucleases; C022535:exoribonuclease II; C091139:ribonuclease HII; D043244:Ribonuclease III; C468366:ribonuclease III, E coli; D016914:Ribonuclease H