This family includes type 2 RNases H from archaea, some of which show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one is involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair.
Feature 1: active site [active site], 4 residue positions
Conserved feature residue pattern:D [DE] D [ED]
Evidence:
Structure:1I3A; Archaeglobus fulgidus RNase HII binds cobalt(III)-hexammine chloride, demonstrating coordination of a divalent metal ion; contacts at 4A.
Comment:The four conserved carboxylates are directly involved in coordinating the metal ion
Jiyao W et al.(2023). "The conserved domain database in 2023.",