1I3A

RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE

Summary for 1I3A

• Entry DOI: 10.2210/pdb1i3a/pdb
• Related: 1I39
• Descriptor: RIBONUCLEASE HII, COBALT HEXAMMINE(III) (3 entities in total)
• Functional Keywords: mixed beta sheet, helix-loop-helix, hydrolase
• Biological source: Archaeoglobus fulgidus
• Cellular location: Cytoplasm (Potential): O29634
• Total number of polymer chains: 1
• Total formula weight: 25554.36

Authors

Chapados, B.R.,Chai, Q.,Hosfield, D.J.,Qiu, J.,Shen, B.,Tainer, J.A. (deposition date: 2001-02-13, release date: 2001-04-11, Last modification date: 2024-04-03)

Primary citation

Chapados, B.R.,Chai, Q.,Hosfield, D.J.,Qiu, J.,Shen, B.,Tainer, J.A.
Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication.
J.Mol.Biol., 307:541-556, 2001

PubMed Abstract: 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.

PubMed: 11254381
DOI: 10.1006/jmbi.2001.4494

Experimental method

X-RAY DIFFRACTION (2.15 Å)