title: Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.
abstract: The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Rob
authors: R
authors: Abdur
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Oksana O
authors: OO
authors: Gerlits
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Jianhua
authors: J
authors: Gan
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Jiansheng
authors: J
authors: Jiang
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Jozef
authors: J
authors: Salon
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Andrey Y
authors: AY
authors: Kovalevsky
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Alexander A
authors: AA
authors: Chumanevich
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Irene T
authors: IT
authors: Weber
authors: Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors: Zhen
authors: Z
authors: Huang
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020029:Base Pairing; D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry* / Q000201:enzymology / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D016914:Ribonuclease H / Q000737:chemistry* / Q000235:genetics; D012643:Selenium / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D009841:Oligonucleotides; D011994:Recombinant Proteins; D012313:RNA; D016914:Ribonuclease H; D012643:Selenium
keywords: DNA and modification; RNase H and RNA cleavage; protein–nucleic acid complexes; selenium derivatization and phasing