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Neighboring group participation in the transition state of human purine nucleoside phosphorylase.

Murkin AS, Birck MR, Rinaldo-Matthis A, Shi W, Taylor EA, Almo SC, Schramm VL
Biochemistry 46 5038-49 (2007)
Related entries: 2a0w, 2a0y, 2oc4, 2oc9, 2on6

Cited: 32 times
EuropePMC logo PMID: 17407325

Abstract

The X-ray crystal structures of human purine nucleoside phosphorylase (PNP) with bound inosine or transition-state analogues show His257 within hydrogen bonding distance of the 5'-hydroxyl. The mutants His257Phe, His257Gly, and His257Asp exhibited greatly decreased affinity for Immucillin-H (ImmH), binding this mimic of an early transition state as much as 370-fold (Km/Ki) less tightly than native PNP. In contrast, these mutants bound DADMe-ImmH, a mimic of a late transition state, nearly as well as the native enzyme. These results indicate that His257 serves an important role in the early stages of transition-state formation. Whereas mutation of His257 resulted in little variation in the PNP x DADMe-ImmH x SO4 structures, His257Phe x ImmH x PO4 showed distortion at the 5'-hydroxyl, indicating the importance of H-bonding in positioning this group during progression to the transition state. Binding isotope effect (BIE) and kinetic isotope effect (KIE) studies of the remote 5'-(3)H for the arsenolysis of inosine with native PNP revealed a BIE of 1.5% and an unexpectedly large intrinsic KIE of 4.6%. This result is interpreted as a moderate electronic distortion toward the transition state in the Michaelis complex with continued development of a similar distortion at the transition state. The mutants His257Phe, His257Gly, and His257Asp altered the 5'-(3)H intrinsic KIE to -3, -14, and 7%, respectively, while the BIEs contributed 2, 2, and -2%, respectively. These surprising results establish that forces in the Michaelis complex, reported by the BIEs, can be reversed or enhanced at the transition state.

Articles - 2a0x mentioned but not cited (3)

  1. Neighboring group participation in the transition state of human purine nucleoside phosphorylase. Murkin AS, Birck MR, Rinaldo-Matthis A, Shi W, Taylor EA, Almo SC, Schramm VL. Biochemistry 46 5038-5049 (2007)
  2. Binding pocket optimization by computational protein design. Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B. PLoS One 7 e52505 (2012)
  3. Molecular docking investigation of the amantadine binding to the enzymes upregulated or downregulated in Parkinson's disease. Ionescu MI. ADMET DMPK 8 149-175 (2020)


Reviews citing this publication (3)

  1. Binding isotope effects: boon and bane. Schramm VL. Curr Opin Chem Biol 11 529-536 (2007)
  2. Enzymatic Transition States and Drug Design. Schramm VL. Chem Rev 118 11194-11258 (2018)
  3. From crystal to compound: structure-based antimalarial drug discovery. Drinkwater N, McGowan S. Biochem J 461 349-369 (2014)

Articles citing this publication (26)

  1. Enzymatic transition states and dynamic motion in barrier crossing. Schwartz SD, Schramm VL. Nat Chem Biol 5 551-558 (2009)
  2. Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme. Silva RG, Murkin AS, Schramm VL. Proc Natl Acad Sci U S A 108 18661-18665 (2011)
  3. Atomic detail of chemical transformation at the transition state of an enzymatic reaction. Saen-Oon S, Quaytman-Machleder S, Schramm VL, Schwartz SD. Proc Natl Acad Sci U S A 105 16543-16548 (2008)
  4. Four generations of transition-state analogues for human purine nucleoside phosphorylase. Ho MC, Shi W, Rinaldo-Matthis A, Tyler PC, Evans GB, Clinch K, Almo SC, Schramm VL. Proc Natl Acad Sci U S A 107 4805-4812 (2010)
  5. Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase. Saen-Oon S, Ghanem M, Schramm VL, Schwartz SD. Biophys J 94 4078-4088 (2008)
  6. Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics. Zoi I, Suarez J, Antoniou D, Cameron SA, Schramm VL, Schwartz SD. J Am Chem Soc 138 3403-3409 (2016)
  7. Third-generation immucillins: syntheses and bioactivities of acyclic immucillin inhibitors of human purine nucleoside phosphorylase. Clinch K, Evans GB, Fröhlich RF, Furneaux RH, Kelly PM, Legentil L, Murkin AS, Li L, Schramm VL, Tyler PC, Woolhouse AD. J Med Chem 52 1126-1143 (2009)
  8. Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. Hirschi JS, Arora K, Brooks CL, Schramm VL. J Phys Chem B 114 16263-16272 (2010)
  9. Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch. Singh V, Peng CS, Li D, Mitra K, Silvestre KJ, Tokmakoff A, Essigmann JM. ACS Chem Biol 9 227-236 (2014)
  10. A beta-fluoroamine inhibitor of purine nucleoside phosphorylase. Mason JM, Murkin AS, Li L, Schramm VL, Gainsford GJ, Skelton BW. J Med Chem 51 5880-5884 (2008)
  11. Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases. Soliman ME, Ruggiero GD, Pernía JJ, Greig IR, Williams IH. Org Biomol Chem 7 460-468 (2009)
  12. Isotope-specific and amino acid-specific heavy atom substitutions alter barrier crossing in human purine nucleoside phosphorylase. Suarez J, Schramm VL. Proc Natl Acad Sci U S A 112 11247-11251 (2015)
  13. L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase. Rinaldo-Matthis A, Murkin AS, Ramagopal UA, Clinch K, Mee SP, Evans GB, Tyler PC, Furneaux RH, Almo SC, Schramm VL. J Am Chem Soc 130 842-844 (2008)
  14. Ribocation transition state capture and rebound in human purine nucleoside phosphorylase. Ghanem M, Murkin AS, Schramm VL. Chem Biol 16 971-979 (2009)
  15. Convergent Mechanistic Features between the Structurally Diverse N- and O-Methyltransferases: Glycine N-Methyltransferase and Catechol O-Methyltransferase. Zhang J, Klinman JP. J Am Chem Soc 138 9158-9165 (2016)
  16. Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases. Soliman ME, Pernía JJ, Greig IR, Williams IH. Org Biomol Chem 7 5236-5244 (2009)
  17. Catalytic site conformations in human PNP by 19F-NMR and crystallography. Suarez J, Haapalainen AM, Cahill SM, Ho MC, Yan F, Almo SC, Schramm VL. Chem Biol 20 212-222 (2013)
  18. Pyrophosphate interactions at the transition states of Plasmodium falciparum and human orotate phosphoribosyltransferases. Zhang Y, Schramm VL. J Am Chem Soc 132 8787-8794 (2010)
  19. Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase. Saen-Oon S, Schramm VL, Schwartz SD. Z Phys Chem (N F) 222 1359-1374 (2008)
  20. Transition-state analysis of Trypanosoma cruzi uridine phosphorylase-catalyzed arsenolysis of uridine. Silva RG, Vetticatt MJ, Merino EF, Cassera MB, Schramm VL. J Am Chem Soc 133 9923-9931 (2011)
  21. Imino-oxy acetic acid dealkylation as evidence for an inner-sphere alcohol intermediate in the reaction catalyzed by peptidylglycine alpha-hydroxylating monooxygenase. McIntyre NR, Lowe EW, Merkler DJ. J Am Chem Soc 131 10308-10319 (2009)
  22. Immucillins in custom catalytic-site cavities. Murkin AS, Clinch K, Mason JM, Tyler PC, Schramm VL. Bioorg Med Chem Lett 18 5900-5903 (2008)
  23. Probing the active site of Corynebacterium callunae starch phosphorylase through the characterization of wild-type and His334-->Gly mutant enzymes. Schwarz A, Brecker L, Nidetzky B. FEBS J 274 5105-5115 (2007)
  24. Ribosyl geometry in the transition state of Streptococcus pneumoniae methylthioadenosine nucleosidase from the 3'-(2)H kinetic isotope effect. Luo M, Schramm VL. J Am Chem Soc 130 11617-11619 (2008)
  25. Constrained bonding environment in the Michaelis complex of Trypanosoma cruzi uridine phosphorylase. Silva RG, Kipp DR, Schramm VL. Biochemistry 51 6715-6717 (2012)
  26. PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design. Noske J, Kynast JP, Lemm D, Schmidt S, Höcker B. Protein Sci 32 e4516 (2023)


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