5ZF6

Crystal structure of the dimeric human PNPase

Summary for 5ZF6

• Entry DOI: 10.2210/pdb5zf6/pdb
• Descriptor: Polyribonucleotide nucleotidyltransferase 1, mitochondrial (2 entities in total)
• Functional Keywords: dimeric human pnpase, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 141425.45

Authors

Yuan, H.S.,Golzarroshan, B. (deposition date: 2018-03-02, release date: 2018-08-22, Last modification date: 2023-11-22)

Primary citation

Golzarroshan, B.,Lin, C.L.,Li, C.L.,Yang, W.Z.,Chu, L.Y.,Agrawal, S.,Yuan, H.S.
Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities.
Nucleic Acids Res., 46:8630-8640, 2018

PubMed Abstract: Human polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'-to-5' exoribonuclease principally located in mitochondria where it is responsible for RNA turnover and import. Mutations in PNPase impair structured RNA transport into mitochondria, resulting in mitochondrial dysfunction and disease. PNPase is a trimeric protein with a doughnut-shaped structure hosting a central channel for single-stranded RNA binding and degradation. Here, we show that the disease-linked human PNPase mutants, Q387R and E475G, form dimers, not trimers, and have significantly lower RNA binding and degradation activities compared to wild-type trimeric PNPase. Moreover, S1 domain-truncated PNPase binds single-stranded RNA but not the stem-loop signature motif of imported structured RNA, suggesting that the S1 domain is responsible for binding structured RNAs. We further determined the crystal structure of dimeric PNPase at a resolution of 2.8 Å and, combined with small-angle X-ray scattering, show that the RNA-binding K homology and S1 domains are relatively inaccessible in the dimeric assembly. Taken together, these results show that mutations at the interface of the trimeric PNPase tend to produce a dimeric protein with destructive RNA-binding surfaces, thus impairing both of its RNA import and degradation activities and leading to mitochondria disorders.

PubMed: 30020492
DOI: 10.1093/nar/gky642

Experimental method

X-RAY DIFFRACTION (2.796 Å)