Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046
Junsoo Kim1, Gerelt-Od Sambalkhundev1, Sulhee Kim2
1Division 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.
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.
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