PDBsum entry 4py5

Hydrolase/DNA/RNA

PDB id: 4py5

Contents

Protein chain

267 a.a.

DNA/RNA

Ligands

SO4 ×7

GOL

Metals

_MG

Waters ×187

PDB id:

4py5

Name:

Hydrolase/DNA/RNA

Title:

Thermovibrio ammonificans rnase h3 in complex with 19-mer RNA/DNA

Structure:

Ribonuclease. Chain: a. Engineered: yes. Mutation: yes. 5'-r( Gp Ap Gp Up Gp Cp Gp Ap Cp Ap Cp Cp Up Gp Ap Up Up Cp C)-3'. Chain: b. Engineered: yes. 5'-d( Gp Gp Ap Ap Tp Cp Ap Gp Gp Tp Gp Tp Cp Gp Cp Ap Cp Tp

Source:

Thermovibrio ammonificans. Organism_taxid: 648996. Strain: hb-1. Gene: theam_0945. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Synthetic: yes

Resolution:

2.10Å R-factor: 0.186 R-free: 0.233

Authors:

M.Figiel,M.Nowotny

Key ref:

M.Figiel and M.Nowotny (2014). Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition. Nucleic Acids Res, 42, 9285-9294. PubMed id: 25016521 DOI: 10.1093/nar/gku615

Date:

26-Mar-14 Release date: 30-Jul-14

Protein chain

E8T217  (E8T217_THEA1) -  Ribonuclease from Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1)

Seq: 270 a.a.

Struc: 267 a.a.*

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

DNA/RNA chains

G-A-G-U-G-C-G-A-C-A-C-C-U-G-A-U-U-C-C 19 bases

G-G-A-A-T-C-A-G-G-T-G-T-C-G-C-A-C-T-C 19 bases

Enzyme reactions

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

DOI no: 10.1093/nar/gku615

Nucleic Acids Res 42:9285-9294 (2014)

PubMed id: 25016521

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.

M.Figiel, M.Nowotny.

ABSTRACT

RNases H participate in the replication and maintenance of genomic DNA. RNase H1 cleaves the RNA strand of RNA/DNA hybrids, and RNase H2 in addition hydrolyzes the RNA residue of RNA-DNA junctions. RNase H3 is structurally closely related to RNases H2, but its biochemical properties are similar to type 1 enzymes. Its unique N-terminal substrate-binding domain (N-domain) is related to TATA-binding protein. Here, we report the first crystal structure of RNase H3 in complex with its RNA/DNA substrate. Just like RNases H1, type 3 enzyme recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation. Moreover, the N-domain recognizes RNA and DNA in a manner that is highly similar to the hybrid-binding domain of RNases H1. Our structure demonstrates a remarkable example of parallel evolution of the elements used in the specific recognition of RNA and DNA.