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Literature summary for 3.1.13.4 extracted from

  • Niedzwiecka, A.; Nilsson, P.; Worch, R.; Stepinski, J.; Darzynkiewicz, E.; Virtanen, A.
    Molecular recognition of mRNA 5' cap by 3' poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins (2016), Biochim. Biophys. Acta, 1864, 331-345 .
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene PARN, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Homo sapiens

Protein Variants

Protein Variants Comment Organism
H449A site-directed mutagenesis, the mutant shows loss of the negative cooperativity between the PARN dimer subunits that is evident for the m7GpppG and m7GTP binding by the wild-type protein Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information model of cooperative ligand binding by PARN dimer, binding kinetics, dissociation constants, and thermodynamics, detailed overview Homo sapiens

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
152400
-
recombinant His-tagged enzyme Homo sapiens

Organism

Organism UniProt Comment Textmining
Homo sapiens O95453
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-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity chromatography Homo sapiens

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information molecular mechanism of 5' cap recognition by PARN, overview. The PARN cap-binding site is bipartite: Trp475 constitutes the essential binding surface for m7G, while the first transcribed nucleoside is bound by the nuclease domain. The enzyme interacts with m7GpppG, m7Gpppm2'OG, m7GTP, GpppG(macro), GpppG(micro), m2_2.7GTP, and m3_2.2.7GTP. Role of His449 in mRNA 5' cap binding, involvement of His449 in sustaining the proper specificity of the enzyme, overview Homo sapiens ?
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?

Subunits

Subunits Comment Organism
dimer secondary structure content predictions for full-length PARN Homo sapiens

Synonyms

Synonyms Comment Organism
PARN
-
Homo sapiens

General Information

General Information Comment Organism
additional information poly(A)-specific ribonuclease (PARN) is a dimeric exoribonuclease that efficiently degrades mRNA 3' poly(A) tails while also simultaneously interacting with the mRNA 5' cap. The mRNA 5' cap structure plays a pivotal role in coordination of eukaryotic translation and mRNA degradation. Molecular recognition of mRNA 5' cap by 3' poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins: 1. the auxiliary biological function of 5' cap binding by the 3' degrading enzyme is accomplished by negative cooperativity of PARN dimer subunits, 2. non-coulombic interactions are major factors in the complex formation, and 3. PARN has versatile activity toward alternative forms of the cap. These characteristics contribute to stabilization of the PARN-cap complex needed for the deadenylation processivity. Fluorescence and NMR spectroscopic analysis. Model of cooperative ligand binding by PARN dimer. Enzyme-ligand (cap and cap analogues) interaction analysis by surface plasmon resonance, local conformational changes of PARN upon 5' mRNA cap binding, small increase in the beta-strand and coil contributions and complex formation in the vicinity of the residues Trp475 and Asp478. PARN seems to recognize the 5' cap in a simple fashion by virtue of the single-sided stacking that is unique among cap-binding proteins Homo sapiens