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Catalytic Site Atlas

CSA LITERATURE entry for 1rdd

E.C. nameribonuclease H
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1rdd
CSA Entries With UniProtID P0A7Y4
CSA Entries With EC Number
PDBe Entry 1rdd
PDBSum Entry 1rdd
MACiE Entry M0163

Literature Report

IntroductionMembers of the RNase H family hydrolyze the P-O3' bond of the RNA strand of an RNA-DNA hybrid duplex in the presence of divalent cations such as Mg(II) and Mn(II). RNase HI is found in E. coli and is structurally homologous to the RNase H domain of HIV-1 reverse transcriptase, a target for anti-HIV therapy.
MechansimThe basic mechanism is SN2-like inline displacement of the 3' end of the scissile phosphate group by a water nucleophile in a single step, passing through a pentavalent transition state.
The water nucleophile is held and activated by His 124, which deprotonates the water molecule, enabling attack as a hydroxide ion. His 124 itself is made more basic by hydrogen bonding to the substrate phosphate group 3' to the scissile phosphodiester bond.
The 3' hydroxyl leaving group is activated as a leaving group by protonation by a water molecule; the water molecule itself is acidified by the Mg(II) cation and the 2' hydroxyl of the substrate ribose 5' to the scissile phosphodiester bond.
The residues Asp 134 and Glu 48 are important for orienting the water molecules.

Catalytic Sites for 1rdd

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA124124macie:sideChainActivates the water nucleophile by deprotonation.

Literature References

Haruki M
Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate.
Biochemistry 2000 39 13939-13944
PubMed: 11076536
Haruki M
Investigating the role of conserved residue Asp134 in Escherichia coli ribonuclease HI by site-directed random mutagenesis.
Eur J Biochem 1994 220 623-631
PubMed: 8125123
Katayanagi K
Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site.
Proteins 1993 17 337-346
PubMed: 8108376