1i39
RNASE HII FROM ARCHAEOGLOBUS FULGIDUS
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OverviewOverview
DNA replication and cellular survival requires efficient removal of RNA, primers during lagging strand DNA synthesis. In eukaryotes, RNA primer, removal is initiated by type 2 RNase H, which specifically cleaves the RNA, portion of an RNA-DNA/DNA hybrid duplex. This conserved type 2 RNase H, family of replicative enzymes shares little sequence similarity with the, well-characterized prokaryotic type 1 RNase H enzymes, yet both possess, similar enzymatic properties. Crystal structures and structure-based, mutational analysis of RNase HII from Archaeoglobus fulgidus, both with, and without a bound metal ion, identify the active site for type 2 RNase H, enzymes that provides the general nuclease activity necessary for, catalysis. The two-domain architecture of type 2 RNase H creates a, positively charged binding groove and links the unique C-terminal, helix-loop-helix cap domain to the active site catalytic domain. This, architectural arrangement apparently couples directional A-form duplex, binding, by a hydrogen-bonding Arg-Lys phosphate ruler motif, to, substrate-discrimination, by a tyrosine finger motif, thereby providing, substrate-specific catalytic activity. Combined kinetic and mutational, analyses of structurally implicated substrate binding residues validate, this binding mode. These structural and mutational results together, suggest a molecular mechanism for type 2 RNase H enzymes for the specific, recognition and cleavage of RNA in the RNA-DNA junction within hybrid, duplexes, which reconciles the broad substrate binding affinity with the, catalytic specificity observed in biochemical assays. In combination with, a recent independent structural analysis, these results furthermore, identify testable molecular hypotheses for the activity and function of, the type 2 RNase H family of enzymes, including structural, complementarity, substrate-mediated conformational changes and, coordination with subsequent FEN-1 activity.
About this StructureAbout this Structure
1I39 is a Single protein structure of sequence from Archaeoglobus fulgidus. Active as Ribonuclease H, with EC number 3.1.26.4 Full crystallographic information is available from OCA.
ReferenceReference
Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication., Chapados BR, Chai Q, Hosfield DJ, Qiu J, Shen B, Tainer JA, J Mol Biol. 2001 Mar 23;307(2):541-56. PMID:11254381
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