ArticleRNA (New York, N.Y.)2008
Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 101 citations in OpenAlex.
- A glycolytic intermediate gatekeeps global mRNA decay in Escherichia coli.Nature communications · 2026Article
- Feedforward miR-181d degradation modulates population variance of methyl-guanine methyl transferase and temozolomide resistance.Cell reports · 2025Article
- Human polynucleotide phosphorylase in mitochondrial RNA metabolism.Bioscience reports · 2025Review
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile.Nucleic acids research · 2025Article
- Selective inhibition of Mycobacterium tuberculosis GpsI unveils a novel strategy to target the RNA metabolism.Nucleic acids research · 2025Article
- Structural insights into human PNPase in health and disease.Nucleic acids research · 2025Article
- D-stem mutation in an essential tRNA increases translation speed at the cost of fidelity.PLoS genetics · 2025Article
- Pathological PNPase variants with altered RNA binding and degradation activity affect the phenotype of bacterial and human cell models.NAR molecular medicine · 2025Article
- Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor.Nucleic acids research · 2024Article
- Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase.American journal of physiology. Cell physiology · 2024Article
- Identification of Ribonuclease Inhibitors for the Control of Pathogenic Bacteria.International journal of molecular sciences · 2024Article
- Structural Insights into the Rrp4 Subunit from the Crystal Structure of theBiomolecules · 2024Article
- Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides.RNA biology · 2024Article
- How RNases Shape Mitochondrial Transcriptomes.International journal of molecular sciences · 2022Review
- [Role of PNPT1 in cardiomyocyte apoptosis induced by oxygen-glucose deprivation].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2022Article
- Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase.International journal of molecular sciences · 2022Review
- Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E.BMC genomics · 2021Article
- Pseudomonas aeruginosa Polynucleotide Phosphorylase Controls Tolerance to Aminoglycoside Antibiotics by Regulating the MexXY Multidrug Efflux Pump.Antimicrobial agents and chemotherapy · 2021Article
- β-Strand-mediated interactions of protein domains.Proteins · 2020Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial polynucleotide phosphorylase (PNPase) plays a major role in mRNA turnover by the degradation of RNA from the 3'- to 5'-ends. Here, we determined the crystal structures of the wild-type and a C-terminal KH/S1 domain-truncated mutant (DeltaKH/S1) of Escherichia coli PNPase at resolutions of 2.6 A and 2.8 A, respectively. The six RNase PH domains of the trimeric PNPase assemble into a ring-like structure containing a central channel. The truncated mutant DeltaKH/S1 bound and cleaved RNA less efficiently with an eightfold reduced binding affinity. Thermal melting and acid-induced trimer dissociation studies, analyzed by circular dichroism and dynamic light scattering, further showed that DeltaKH/S1 formed a less stable trimer than the full-length PNPase. The crystal structure of DeltaKH/S1 is more expanded, containing a slightly wider central channel than that of the wild-type PNPase, suggesting that the KH/S1 domain helps PNPase to assemble into a more compact trimer, and it regulates the channel size allosterically. Moreover, site-directed mutagenesis of several arginine residues in the channel neck regions produced defective PNPases that either bound and cleaved RNA less efficiently or generated longer cleaved oligonucleotide products, indicating that these arginines were involved in RNA binding and processive degradation. Taking these results together, we conclude that the constricted central channel and the basic-charged residues in the channel necks of PNPase play crucial roles in trapping RNA for processive exonucleolytic degradation.
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