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Literature summary for 2.7.7.8 extracted from

  • 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 (2012), Nucleic Acids Res., 40, 4146-4157.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21-CodonPlus (DE3)-RIPL Homo sapiens

Crystallization (Commentary)

Crystallization (Comment) Organism
wild-type and S1 domain-truncated hPNPase, hanging-drop vapor diffusion method, mixxing of 0.001 ml of 10 mg/ml protein in 50 mM Tris, pH 8.0, and 150 mM NaCl, with 0.001 ml of reservoir solution containing 0.1 M citrate, pH 5.0, 10% v/v 2-propanol and 26% v/v PEG 400, room temperature, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement method Homo sapiens

Protein Variants

Protein Variants Comment Organism
G622D site-directed mutagenesis Homo sapiens
additional information generation of a S1 domain-lacking mutant enzyme, domain organization of full-length and S1 domain-truncated hPNPase. overview. Full-length and DELTAS1 hPNPase cleave the poly(A)12 and poly(U)12 RNA with similar activities and DELTAS1 hPNPase cleaves ssRNA substrate almost as efficiently as full-length PNPase Homo sapiens

Localization

Localization Comment Organism GeneOntology No. Textmining
exosome structure of the S1 pore in exosomes and the KH pore in hPNPase, overview Homo sapiens
-
-
additional information KH pore in PNPase versus S1 pore in exosomes Homo sapiens
-
-

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Homo sapiens

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
80900
-
3 * 80900, about, sequence calculation, the trimeric hPNPase has a hexameric ring-like structure formed by six RNase PH domains, capped with a trimeric KH pore, the enzyme has a conserved GXXG motif in the KH domain, structural model of hPNPase, overview Homo sapiens
240000
-
recombinant enzyme, gel filtration Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
RNAn+1 + phosphate Homo sapiens the enzyme catalyzes the processive phosphorolysis of RNA by using an inorganic phosphate to cleave the phosphodiester linkage at the 3'-end of a RNA chain RNAn + a nucleoside diphosphate
-
?

Organism

Organism UniProt Comment Textmining
Homo sapiens G8TCS8
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21-CodonPlus (DE3)-RIPL by nickel affinty chromatography and gel filtration Homo sapiens

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information full-length and DELTAS1 hPNPase cleave the poly(A)12 and poly(U)12 RNA with similar activities and DELTAS1 hPNPase cleaves ssRNA substrate almost as efficiently as full-length PNPase Homo sapiens ?
-
?
RNAn+1 + phosphate the enzyme catalyzes the processive phosphorolysis of RNA by using an inorganic phosphate to cleave the phosphodiester linkage at the 3'-end of a RNA chain Homo sapiens RNAn + a nucleoside diphosphate
-
?
RNAn+1 + phosphate the functional trimeric phosphorylase is capable of digesting single-stranded RNA to produce final products of about 4 nt in length Homo sapiens RNAn + a nucleoside diphosphate
-
?

Subunits

Subunits Comment Organism
More domain organization of full-length and S1 domain-truncated hPNPase. overview Homo sapiens
trimer 3 * 80900, about, sequence calculation, the trimeric hPNPase has a hexameric ring-like structure formed by six RNase PH domains, capped with a trimeric KH pore, the enzyme has a conserved GXXG motif in the KH domain, structural model of hPNPase, overview Homo sapiens

Synonyms

Synonyms Comment Organism
PNPase
-
Homo sapiens
polynucleotide phosphorylase
-
Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Homo sapiens

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Homo sapiens

General Information

General Information Comment Organism
additional information the C-terminal S1 domain is not critical for RNA binding, and conversely, the conserved GXXG motif in the KH domain directly participates in RNA binding in hPNPase. The enzyme uses a KH pore to trap a long RNA 3' tail that is further delivered into an RNase PH channel for the degradation process. The three KH domains form a KH pore situated on the top of the hexameric ring-like structure. The KH pore extends the central channel formed by the RNase PH domains and is involved in the binding of RNA substrates, which are further delivered to the active site located within the central channel. Structural RNA with short 3' tails are, on the other hand, transported but not digested by hPNPase. Structural model of hPNPase, overview Homo sapiens
physiological function human polynucleotide phosphorylase 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 Homo sapiens