Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation

Chia Liang Lin1,2, Yi-Ting Wang2, Wei-Zen Yang2, Yu-Yuan Hsiao2 and Hanna S. Yuan2,3,*
1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, 2Institute of
Molecular Biology, Academia Sinica, Taipei 11529 and 3Graduate Institute of Biochemistry and Molecular
Biology, National Taiwan University, Taipei 10051, Taiwan, R.O.C.
ABSTRACT
Human polynucleotide phosphorylase (hPNPase) is a 30-to-50 exoribonuclease that degrades specific mRNA and miRNA, and imports RNA into mitochondria, and thus regulates diverse physiological processes, including cellular senescence and homeostasis. However, the RNA-processing mechanism by hPNPase, particularly how RNA is bound via its various domains, remains obscure. Here, we report the crystal structure of an S1 domain-truncated hPNPase at a resolution of 2.1A ° .
The trimeric hPNPase has a hexameric ring-like structure formed by six RNase PH domains, capped with a trimeric KH pore. Our biochemical and mutagenesis studies suggest that the S1 domain is not critical for RNA binding, and conversely, that the conserved GXXG motif in the KH domain directly participates in RNA binding in
hPNPase. Our studies thus provide structural and functional insights into hPNPase, which uses a KH pore to trap a long RNA 30 tail that is further delivered into an RNase PH channel for the degradation process. Structural RNA with short 30 tails are, on the other hand, transported but not digested by hPNPase.
NAR_2012
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