6DPP

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C

Summary for 6DPP

• Entry DOI: 10.2210/pdb6dpp/pdb
• Group deposition: Cleavage of RNA by B. Halodurans Ribonuclease H1 (G_1001001)
• Descriptor: Ribonuclease H, 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3', 5'-R(P*CP*G)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3', ... (10 entities in total)
• Functional Keywords: protein-rna-dna complex, double helix, rna hydrolysis, in crystallo catalysis, metal dependent catalysis, monovalent cations, divalent cations, hydrolase-rna-dna complex, hydrolase/rna/dna
• Biological source: Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125); More
• Total number of polymer chains: 4
• Total formula weight: 20540.12

Authors

Samara, N.L.,Yang, W. (deposition date: 2018-06-09, release date: 2018-08-15, Last modification date: 2023-10-11)

Primary citation

Samara, N.L.,Yang, W.
Cation trafficking propels RNA hydrolysis.
Nat. Struct. Mol. Biol., 25:715-721, 2018

PubMed Abstract: Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg ions and an additional K failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K and a third Mg, which replaced the first K and departed immediately after cleavage. A third transient Mg has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.

PubMed: 30076410
DOI: 10.1038/s41594-018-0099-4

Experimental method

X-RAY DIFFRACTION (1.45 Å)