4PY5

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

Summary for 4PY5

• Entry DOI: 10.2210/pdb4py5/pdb
• Descriptor: Ribonuclease, 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3', 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3', ... (7 entities in total)
• Functional Keywords: rnase h fold, rna/dna hybrid, hydrolase-dna-rna complex, hydrolase/dna/rna
• Biological source: Thermovibrio ammonificans
• Cellular location: Cytoplasm (By similarity): E8T217
• Total number of polymer chains: 3
• Total formula weight: 42989.96

Authors

Figiel, M.,Nowotny, M. (deposition date: 2014-03-26, release date: 2014-07-30, Last modification date: 2024-11-20)

Primary citation

Figiel, M.,Nowotny, M.
Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.
Nucleic Acids Res., 42:9285-9294, 2014

PubMed 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.

PubMed: 25016521
DOI: 10.1093/nar/gku615

Experimental method

X-RAY DIFFRACTION (2.1 Å)