6DPE

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 20 mM Mn2+ and 200 mM K+ for 40 s at 21 C

6DPE の概要

• エントリーDOI: 10.2210/pdb6dpe/pdb
• Group deposition: Cleavage of RNA by B. Halodurans Ribonuclease H1 (G_1001001)
• 分子名称: Ribonuclease H, TRIETHYLENE GLYCOL, RNA (5'-R(*AP*CP*AP*U)-3'), ... (11 entities in total)
• 機能のキーワード: protein-rna-dna complex, double helix, rna hydrolysis, in crystallo catalysis, metal dependent catalysis, monovalent cations, divalent cations, hydrolase-dna-rna complex, hydrolase/dna/rna
• 由来する生物種: Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 20994.22

構造登録者

Samara, N.L.,Yang, W. (登録日: 2018-06-09, 公開日: 2018-08-15, 最終更新日: 2023-10-11)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.56 Å)