Sequence and comparative structural analysis of the murine leukaemia virusamphotropic strain 4070A RNase H domain

The sequence of a 900-nucleotide segment (encoding part of the reverse tran scriptase, including the entire RNase H domain) of the pol gene of the muri ne leukaemia virus (MLV) amphotropic strain 4070A is presented. Align ment of the inferred 4070A RNase H amino acid sequence (157 residues) with other MLV RNase H sequences revealed only minor differences compared with the di vergence between other retroviral and prokaryotic or eukaryotic RNase H seq uences. Only 10 residues were invariant across the entire sample set, but s econdary structure predictions for the enzymes from E. coli, yeast, human l iver and diverse retroviruses (HIV, Rous sarcoma virus, foamy viruses) supp orted, in every case, the five P-strands (1 to 5) and four or five alpha-he lices (A, B/C, D, E) that have been identified by crystallography in the RN ase H domain of HIV-1 reverse transcriptase and in E. coli RNase H. In the case of MLV, analysis of the RNase H domain sequences inferred from 10 diff erent strains (including the amphotropic 4070A) predicted all five alpha-he lices (A-E), as well as beta-strands 1 and 5. However, the N-terminal segme nt (residues 1-40) was predicted, without exception and with high probabili ty, to fold uniquely into one (or two adjacent) alpha-helix(es) encompassin g residues 13-37, instead of the three beta-strands known to exist in the H IV-1 and E. coli enzymes. The unerring consistency between the known and pr edicted structures of the HIV-1 and E. coli enzymes, and the prediction of the same structural elements (including beta-strands 1-3 within the N-termi nal segment) for all other (non-MLV) RNase H proteins examined in this stud y, suggests that the N-terminal segment of the MLV RNase H domain assumes a conformation distinct from that of other retroviral and cellular RNase H m olecules. An additional (sixth) beta-strand was also predicted uniquely wit hin the C-terminal region of foamy virus RNase H domains.