3U1K: Crystal Structure Of Human Pnpase

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 A. 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.
PDB ID: 3U1KDownload
MMDB ID: 96917
PDB Deposition Date: 2011/9/30
Updated in MMDB: 2013/06
Experimental Method:
x-ray diffraction
Resolution: 2.13  Å
Source Organism:
Similar Structures:
Biological Unit for 3U1K: trimeric; determined by author and by software (PISA)
Molecular Components in 3U1K
Label Count Molecule
Proteins (3 molecules)
Polyribonucleotide Nucleotidyltransferase 1, Mitochondrial(Gene symbol: PNPT1)
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB