4H8K

Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid

Summary for 4H8K

• Entry DOI: 10.2210/pdb4h8k/pdb
• Descriptor: Ribonuclease H, RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'), ... (4 entities in total)
• Functional Keywords: rnase h, ribonuclease h rna dna hybrid, hydrolase, ribonuclease h, hydrolase-dna-rna complex, hydrolase/dna/rna
• Biological source: uncultured organism; More
• Total number of polymer chains: 4
• Total formula weight: 40005.41

Authors

Nguyen, T.N.,You, D.J.,Matsumoto, H.,Kanaya, E.,Kanaya, S. (deposition date: 2012-09-23, release date: 2013-09-25, Last modification date: 2023-11-08)

Primary citation

Nguyen, T.N.,You, D.J.,Matsumoto, H.,Kanaya, E.,Koga, Y.,Kanaya, S.
Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid
J.Struct.Biol., 182:144-154, 2013

PubMed Abstract: LC11-RNase H1 is a Sulfolobus tokodaii RNase H1 (Sto-RNase H1) homologue isolated by metagenomic approach. In this study, the crystal structure of LC11-RNase H1 in complex with an RNA/DNA substrate was determined. Unlike Bacillus halodurans RNase H1 without hybrid binding domain (HBD) (Bh-RNase HC) and human RNase H1 without HBD (Hs-RNase HC), LC11-RNase H1 interacts with four non-consecutive 2'-OH groups of the RNA strand. The lack of interactions with four consecutive 2'-OH groups leads to a dramatic decrease in the ability of LC11-RNase H1 to cleave the DNA-RNA-DNA/DNA substrate containing four ribonucleotides as compared to those to cleave the substrates containing five and six ribonucleotides. The interaction of LC11-RNase H1 with the DNA strand is also different from those of Bh-RNase HC and Hs-RNase HC. Beside the common phosphate-binding pocket, LC11-RNase H1 has a unique DNA-binding channel. Furthermore, the active-site residues of LC11-RNase H1 are located farther away from the scissile phosphate group than those of Bh-RNase HC and Hs-RNase HC. Modeling of Sto-RNase H1 in complex with the 14bp RNA/DNA substrate, together with the structure-based mutational analyses, suggest that the ability of Sto-RNase H1 to cleave double-stranded RNA is dependent on the local conformation of the basic residues located at the DNA binding site.

PubMed: 23500886
DOI: 10.1016/j.jsb.2013.02.018

Experimental method

X-RAY DIFFRACTION (2.3 Å)