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Literature summary for 2.4.2.1 extracted from

  • Roca, M.; Moliner, V.; Tunon, I.
    Origin of enzymatic kinetic isotope effects in human purine nucleoside phosphorylase (2018), ACS Catal., 8, 815-827 .
No PubMed abstract available
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KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information kinetic analysis, kinetic isotope effeccts, quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, overview Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
inosine + phosphate Homo sapiens
-
 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r

Organism

Organism UniProt Comment Textmining
Homo sapiens P00491
-
-

Reaction

Reaction Comment Organism Reaction ID
purine ribonucleoside + phosphate = purine + alpha-D-ribose 1-phosphate the structure of hPNP is a homotrimer with the catalytic sites near the subunit interfaces. The ternary complex of hPNP includes the binding of inosine and hydrogen phosphate to the active site. The reaction consists of a phosphorolysis at C1' of inosine's ribose with inversion of stereochemistry at this position. Reaction occurs via an SN1-like mechanism where hydrogen phosphate nucleophile and the purine base leaving group are separated from the oxocarbenium ion, defining a dissociative transition state. It has to be pointed out that the reaction involves annihilation of charges in going from the reactant state to the product state. Reaction mechanism analysis, quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, detailed overview Homo sapiens
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
inosine + phosphate
-
 Homo sapiens hypoxanthine + alpha-D-ribose 1-phosphate
-
 r

Subunits

Subunits Comment Organism
homotrimer the structure of hPNP is a homotrimer with the catalytic sites near the subunit interfaces. The ternary complex of hPNP includes the binding of inosine and hydrogen phosphate to the active site Homo sapiens

Synonyms

Synonyms Comment Organism
hPNP
-
 Homo sapiens
PNP
-
 Homo sapiens
purine nucleoside phosphorylase
-
 Homo sapiens

General Information

General Information Comment Organism
additional information effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, the mechanism of the hPNP enzymeis investigated and the dynamic effects by means of the calculation of the recrossing transmission coefficient. The simulations reveal that the chemical reaction is slightly slower in the heavy enzyme than in its light counterpart enzyme because protein motions coupled to the reaction coordinate are slower. Thus, protein dynamics have a small but measurable effect on the chemical reaction rate Homo sapiens