Polynucleotidyl Transferase RNase HLike Fold

The structures of a number of enzymes involved in polynucleotide transfer have been observed to have the same basic fold as ribonu-clease H (RNaseH; Katayanagi et al., 1990, 1992; Yang et al., 1990). Members of this family include RNase H, retroviral integrase, Holiday junction RuvC resolvase, TN5 transposase, the RNase H domain of retroviral reverse transcriptase, a core fragment of bacteriaphage Mu transposase, and the 3'-5' exonuclease domains from several DNA polymerase structures, including the Klenow fragment (Ollis et al., 1985; Davies et al., 1991, 2000; Ariyoshi et al., 1994; Dyda et al., 1994; Rice and Mizuuchi, 1995). The sequence identity among family members is generally <15%. At the center of the structure is a five-stranded P-sheet, aligned with a strand order of 3-2-1-4-5. The second strand is antiparallel to the other four strands (Fig. 17.1.31). The number and location of the helices are less conserved than the central P-sheet. Helices A and E are topologically more conserved than the other helices. They are located between strands 3 and 4, and at the C-terminal of strand 5 in sequence, primarily interacting with the central P-sheet. The number of helices between strands 4 and 5 varies, as do the helices after helix E (Fig. 17.1.31). The family can be further divided into RNase- (e.g., HIV-1 reverse transcriptase RNase H, E. coli RNase H, Archeon Class II RNase H) and integrase-like structures (e.g., integrase, Mu A transposase, RuvC) with greater structure resemblance observed between the members of each subclass. Limited structural homology, particularly among the central five-stranded P-sheet, is also observed with Mut S domain II, actin-like ATPase domains, and ribosomal proteins L18 and S11.

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