title: Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid.
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.
authors.affiliation: Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Tri-Nhan
authors.initials: TN
authors.lastname: Nguyen
authors.forename: Dong-Ju
authors.initials: DJ
authors.lastname: You
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Matsumoto
authors.forename: Eiko
authors.initials: E
authors.lastname: Kanaya
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Koga
authors.forename: Shigenori
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D003460:Crystallization; D019641:DNA, Archaeal / Q000737:chemistry* / Q000378:metabolism; D054892:Metagenome / Q000235:genetics*; D008958:Models, Molecular; D010957:Plasmids / Q000235:genetics; D011487:Protein Conformation; D019642:RNA, Archaeal / Q000737:chemistry* / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism; D016944:Sulfolobus / Q000201:enzymology*; D014961:X-Ray Diffraction
chemical_list: D019641:DNA, Archaeal; D019642:RNA, Archaeal; D016914:Ribonuclease H; C078856:ribonuclease HI