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6DOG

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 600 s at 21 C

Summary for 6DOG
Entry DOI10.2210/pdb6dog/pdb
Group depositionCleavage of RNA by B. Halodurans Ribonuclease H1 (G_1001001)
DescriptorRibonuclease H, TRIETHYLENE GLYCOL, RNA (5'-R(*AP*CP*AP*U)-3'), ... (11 entities in total)
Functional Keywordsprotein-rna-dna complex, double helix, rna hydrolysis, in crystallo catalysis, metal dependent catalysis, monovalent cations, divalent cations, hydrolase, hydrolase-rna-dna complex, hydrolase/rna/dna
Biological sourceBacillus halodurans
More
Total number of polymer chains4
Total formula weight21517.36
Authors
Samara, N.L.,Yang, W. (deposition date: 2018-06-09, release date: 2018-08-15, Last modification date: 2023-10-11)
Primary citationSamara, N.L.,Yang, W.
Cation trafficking propels RNA hydrolysis.
Nat. Struct. Mol. Biol., 25:715-721, 2018
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.285 Å)
Structure validation

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