title: Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046.
abstract: RNase H fold protein PF2046 of Pyrococcus furiosus is a 3'-5' ssDNA exonuclease that cleaves after the second nucleotide from the 3' end of ssDNA and prefers poly-dT over poly-dA as a substrate. In our crystal structure of PF2046 complexed with an oligonucleotide of four thymidine nucleotides (dT4), PF2046 accommodates dT4 tightly in a groove and imposes steric hindrance on dT4 mainly by Phe220 such that dT4 assumes the A-form. As poly-dA prefer B-form due to the stereochemical restrictions, the A-form ssDNA binding by PF2046 should disfavor the processing of poly-dA. Phe220 variants display reduced activity toward poly-dA and the A-form appears to be a prerequisite for the processing by PF2046.
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea.
authors: Junsoo
authors: J
authors: Kim
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea.
authors: Gerelt-Od
authors: GO
authors: Sambalkhundev
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
authors: Sulhee
authors: S
authors: Kim
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
authors: Jonghyeon
authors: J
authors: Son
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
authors: Ah-Reum
authors: AR
authors: Han
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
authors: Sul-Min
authors: SM
authors: Ko
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea. Electronic address: chahong@korea.ac.kr.
authors: Kwang Yeon
authors: KY
authors: Hwang
authors: Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea. Electronic address: dreadco@gmail.com.
authors: Woo Cheol
authors: WC
authors: Lee
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D003460:Crystallization; D018360:Crystallography, X-Ray; D004260:DNA Repair; D004277:DNA, Single-Stranded / Q000737:chemistry*; D005092:Exonucleases / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D009154:Mutation; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D020027:Pyrococcus furiosus / Q000201:enzymology*; D016914:Ribonuclease H / Q000737:chemistry*; D013379:Substrate Specificity; D014961:X-Ray Diffraction
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D005092:Exonucleases; D016914:Ribonuclease H
keywords: A-form; Exonuclease; RNase H; ssDNA