PDBsum entry 6dpm

Hydrolase/RNA/DNA

PDB id: 6dpm

Contents

Protein chain

136 a.a.

DNA/RNA

Ligands

_DC-_DG

GOL ×4

EDO ×4

Metals

_RB ×6

_MG ×2

_CL ×3

Waters ×181

PDB id:

6dpm

Name:

Hydrolase/RNA/DNA

Title:

Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA/DNA hybrid: reaction in 10 mm mg2+ and 200 mm rb+ for 1800 s at 21 c

Structure:

Ribonuclease h. Chain: a. Fragment: catalytic domain. Synonym: rnase h. Engineered: yes. Mutation: yes. 5'-r( Ap Cp Ap U)-3' portion of cleaved RNA 5'- r( Ap Cp Ap Up Cp G)-3'. Chain: b.

Source:

Bacillus halodurans. Organism_taxid: 86665. Gene: rnha, bh0863. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

1.68Å R-factor: 0.162 R-free: 0.199

Authors:

N.L.Samara,W.Yang

Key ref:

N.L.Samara and W.Yang (2018). Cation trafficking propels RNA hydrolysis. Nat Struct Mol Biol, 25, 715-721. PubMed id: 30076410 DOI: 10.1038/s41594-018-0099-4

Date:

09-Jun-18 Release date: 15-Aug-18

Protein chain

Q9KEI9  (RNH1_BACHD) -  Ribonuclease H from Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)

Seq: 196 a.a.

Struc: 136 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-C-A-U 4 bases

C-G-A-T-G-T 6 bases

Enzyme reactions

• Enzyme class: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

DOI no: 10.1038/s41594-018-0099-4

Nat Struct Mol Biol 25:715-721 (2018)

PubMed id: 30076410

Cation trafficking propels RNA hydrolysis.

N.L.Samara, W.Yang.

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.