Abstract：
:Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg2+ 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 Mg2+ 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 Mg2+, which replaced the first K+ and departed immediately after cleavage. A third transient Mg2+ 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.
journal_name
Nat Struct Mol Bioljournal_title
Nature structural & molecular biologyauthors
Samara NL,Yang Wdoi
10.1038/s41594-018-0099-4subject
Has Abstractpub_date
2018-08-01 00:00:00pages
715-721issue
8eissn
1545-9993issn
1545-9985pii
10.1038/s41594-018-0099-4journal_volume
25pub_type
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