3U1K

Crystal structure of human PNPase

Summary for 3U1K

• Entry DOI: 10.2210/pdb3u1k/pdb
• Descriptor: Polyribonucleotide nucleotidyltransferase 1, mitochondrial, CITRIC ACID (3 entities in total)
• Functional Keywords: rnase ph, kh domain, exoribonuclease, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q8TCS8
• Total number of polymer chains: 4
• Total formula weight: 276775.43

Authors

Lin, C.L.,Yuan, H.S. (deposition date: 2011-09-30, release date: 2012-02-01, Last modification date: 2023-11-01)

Primary citation

Lin, C.L.,Wang, Y.-T.,Yang, W.-Z.,Hsiao, Y.-Y.,Yuan, H.S.
Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation
Nucleic Acids Res., 40:4146-4157, 2012

PubMed Abstract: 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.

PubMed: 22210891
DOI: 10.1093/nar/gkr1281

Experimental method

X-RAY DIFFRACTION (2.13 Å)