Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis

A. Fedorov, W. Shi, G. Kicska, Vern L. Schramm, Steven C. Almo, E. Fedorov, P. C. Tyler, R. H. Furneaux, J. C. Hanson, G. J. Gainsford, J. Z. Larese

Research output: Contribution to journalArticle

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Abstract

Immucillin-H [ImmH; (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol] is a 23 pM inhibitor of bovine purine nucleoside phosphorylase (PNP) specifically designed as a transition state mimic [Miles, R. W., Tyler, P. C., Furneaux, R. H., Bagdassarian, C. K., and Schramm, V. L. (1998) Biochemistry 37, 8615-8621]. Cocrystals of PNP and the inhibitor are used to provide structural information for each step through the reaction coordinate of PNP. The X-ray crystal structure of free ImmH was solved at 0.9 Å resolution, and a complex of PNP·ImmH·PO4 was solved at 1.5 Å resolution. These structures are compared to previously reported complexes of PNP with substrate and product analogues in the catalytic sites and with the experimentally determined transition state structure. Upon binding, ImmH is distorted to a conformation favoring ribosyl oxocarbenium ion formation. Ribosyl destabilization and transition state stabilization of the ribosyl oxocarbenium ion occur from neighboring group interactions with the phosphate anion and the 5′-hydroxyl of the ribosyl group. Leaving group activation of hypoxanthine involves hydrogen bonds to 06, N1, and N7 of the purine ring. Ordered water molecules provide a proton transfer bridge to O6 and N7 and permit reversible formation of these hydrogen bonds. Contacts between PNP and catalytic site ligands are shorter in the transition state analogue complex of PNP·ImmH·PO4 than in the Michaelis complexes of PNP·inosine·SO4 or PNP·hypoxanthine·ribose 1-PO4. Reaction coordinate motion is dominated by translation of the carbon 1' of ribose between relatively fixed phosphate and purine groups. Purine and pyrimidine phosphoribosyltransferases and nucleoside N-ribosyl hydrolases appear to operate by a similar mechanism.

Original languageEnglish (US)
Pages (from-to)853-860
Number of pages8
JournalBiochemistry
Volume40
Issue number4
DOIs
StatePublished - Jan 30 2001

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Purine-Nucleoside Phosphorylase
Catalysis
Hydrogen
Catalytic Domain
Hydrogen bonds
Ribitol
Phosphates
Pyrimidine Nucleosides
Ions
Purine Nucleosides
Biochemistry
Hypoxanthine
Proton transfer
Ribose
Hydrolases
Hydroxyl Radical
Anions
Conformations
Protons
Carbon

ASJC Scopus subject areas

  • Biochemistry

Cite this

Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. / Fedorov, A.; Shi, W.; Kicska, G.; Schramm, Vern L.; Almo, Steven C.; Fedorov, E.; Tyler, P. C.; Furneaux, R. H.; Hanson, J. C.; Gainsford, G. J.; Larese, J. Z.

In: Biochemistry, Vol. 40, No. 4, 30.01.2001, p. 853-860.

Research output: Contribution to journalArticle

Fedorov, A, Shi, W, Kicska, G, Schramm, VL, Almo, SC, Fedorov, E, Tyler, PC, Furneaux, RH, Hanson, JC, Gainsford, GJ & Larese, JZ 2001, 'Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis', Biochemistry, vol. 40, no. 4, pp. 853-860. https://doi.org/10.1021/bi002499f
Fedorov, A. ; Shi, W. ; Kicska, G. ; Schramm, Vern L. ; Almo, Steven C. ; Fedorov, E. ; Tyler, P. C. ; Furneaux, R. H. ; Hanson, J. C. ; Gainsford, G. J. ; Larese, J. Z. / Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. In: Biochemistry. 2001 ; Vol. 40, No. 4. pp. 853-860.
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abstract = "Immucillin-H [ImmH; (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol] is a 23 pM inhibitor of bovine purine nucleoside phosphorylase (PNP) specifically designed as a transition state mimic [Miles, R. W., Tyler, P. C., Furneaux, R. H., Bagdassarian, C. K., and Schramm, V. L. (1998) Biochemistry 37, 8615-8621]. Cocrystals of PNP and the inhibitor are used to provide structural information for each step through the reaction coordinate of PNP. The X-ray crystal structure of free ImmH was solved at 0.9 {\AA} resolution, and a complex of PNP·ImmH·PO4 was solved at 1.5 {\AA} resolution. These structures are compared to previously reported complexes of PNP with substrate and product analogues in the catalytic sites and with the experimentally determined transition state structure. Upon binding, ImmH is distorted to a conformation favoring ribosyl oxocarbenium ion formation. Ribosyl destabilization and transition state stabilization of the ribosyl oxocarbenium ion occur from neighboring group interactions with the phosphate anion and the 5′-hydroxyl of the ribosyl group. Leaving group activation of hypoxanthine involves hydrogen bonds to 06, N1, and N7 of the purine ring. Ordered water molecules provide a proton transfer bridge to O6 and N7 and permit reversible formation of these hydrogen bonds. Contacts between PNP and catalytic site ligands are shorter in the transition state analogue complex of PNP·ImmH·PO4 than in the Michaelis complexes of PNP·inosine·SO4 or PNP·hypoxanthine·ribose 1-PO4. Reaction coordinate motion is dominated by translation of the carbon 1' of ribose between relatively fixed phosphate and purine groups. Purine and pyrimidine phosphoribosyltransferases and nucleoside N-ribosyl hydrolases appear to operate by a similar mechanism.",
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AU - Fedorov, A.

AU - Shi, W.

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AU - Schramm, Vern L.

AU - Almo, Steven C.

AU - Fedorov, E.

AU - Tyler, P. C.

AU - Furneaux, R. H.

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AU - Larese, J. Z.

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N2 - Immucillin-H [ImmH; (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol] is a 23 pM inhibitor of bovine purine nucleoside phosphorylase (PNP) specifically designed as a transition state mimic [Miles, R. W., Tyler, P. C., Furneaux, R. H., Bagdassarian, C. K., and Schramm, V. L. (1998) Biochemistry 37, 8615-8621]. Cocrystals of PNP and the inhibitor are used to provide structural information for each step through the reaction coordinate of PNP. The X-ray crystal structure of free ImmH was solved at 0.9 Å resolution, and a complex of PNP·ImmH·PO4 was solved at 1.5 Å resolution. These structures are compared to previously reported complexes of PNP with substrate and product analogues in the catalytic sites and with the experimentally determined transition state structure. Upon binding, ImmH is distorted to a conformation favoring ribosyl oxocarbenium ion formation. Ribosyl destabilization and transition state stabilization of the ribosyl oxocarbenium ion occur from neighboring group interactions with the phosphate anion and the 5′-hydroxyl of the ribosyl group. Leaving group activation of hypoxanthine involves hydrogen bonds to 06, N1, and N7 of the purine ring. Ordered water molecules provide a proton transfer bridge to O6 and N7 and permit reversible formation of these hydrogen bonds. Contacts between PNP and catalytic site ligands are shorter in the transition state analogue complex of PNP·ImmH·PO4 than in the Michaelis complexes of PNP·inosine·SO4 or PNP·hypoxanthine·ribose 1-PO4. Reaction coordinate motion is dominated by translation of the carbon 1' of ribose between relatively fixed phosphate and purine groups. Purine and pyrimidine phosphoribosyltransferases and nucleoside N-ribosyl hydrolases appear to operate by a similar mechanism.

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