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

Human polynucleotide phosphorylase (hPNPase) is a 3'-to-5' 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 h...

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Bibliographic Details
Published in:Nucleic acids research 2012-05, Vol.40 (9), p.4146-4157
Main Authors: Lin, Chia Liang, Wang, Yi-Ting, Yang, Wei-Zen, Hsiao, Yu-Yuan, Yuan, Hanna S
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Channel pores
Crystal structure
Crystallography, X-Ray
Exoribonucleases - chemistry
Exoribonucleases - genetics
Exoribonucleases - metabolism
Homeostasis
Humans
miRNA
Mitochondria
Models, Molecular
Molecular Sequence Data
mRNA
Mutagenesis
polynucleotide phosphorylase
Polyribonucleotide Nucleotidyltransferase - chemistry
Polyribonucleotide Nucleotidyltransferase - genetics
Polyribonucleotide Nucleotidyltransferase - metabolism
Protein Binding
Protein Structure, Tertiary
Ribonuclease
RNA - metabolism
Senescence
Sequence Deletion
Structural Biology
Structure-function relationships
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Summary:Human polynucleotide phosphorylase (hPNPase) is a 3'-to-5' 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 2.1 Å. 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 3' tail that is further delivered into an RNase PH channel for the degradation process. Structural RNA with short 3' tails are, on the other hand, transported but not digested by hPNPase.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr1281