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Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase.

Ding X, Rasmussen BF, Petsko GA, Ringe D
Biochemistry 33 9285-93 (1994)
Cited: 41 times
EuropePMC logo PMID: 8049229

Abstract

The method of X-ray crystallographic cryoenzymology has been used to determine the crystal structure of a kinetically significant species on the reaction pathway of a crystalline enzyme. The structure of a specific acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of the N-carbobenzoxy-L-alanine p-nitrophenyl ester has been determined and refined against X-ray diffraction data at 2.3-A resolution. The difference Fourier electron density map clearly shows electron density for the trapped acyl-enzyme. The acyl-enzyme was formed at -26 degrees C and was stabilized at -55 degrees C during data collection, taking advantage of the glass transition in protein dynamics that occurs at around -50 degrees C.

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  1. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M. BMC Struct Biol 6 19 (2006)
  2. Fpocket: an open source platform for ligand pocket detection. Le Guilloux V, Schmidtke P, Tuffery P. BMC Bioinformatics 10 168 (2009)
  3. PocketPicker: analysis of ligand binding-sites with shape descriptors. Weisel M, Proschak E, Schneider G. Chem Cent J 1 7 (2007)
  4. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. Cao C, Xu S. Sci Rep 6 33232 (2016)
  5. A new definition and properties of the similarity value between two protein structures. Saberi Fathi SM. J Biol Phys 42 621-636 (2016)


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  1. The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it. Ringe D, Petsko GA. Biophys. Chem. 105 667-680 (2003)
  2. Protein dynamics and conformational transitions in allosteric proteins. Jardetzky O. Prog. Biophys. Mol. Biol. 65 171-219 (1996)
  3. Freeze trapping of reaction intermediates. Moffat K, Henderson R. Curr. Opin. Struct. Biol. 5 656-663 (1995)
  4. Observation of unstable species in enzyme-catalyzed transformations using protein crystallography. Petsko GA, Ringe D. Curr Opin Chem Biol 4 89-94 (2000)
  5. Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening. Stoddard BL. Pharmacol. Ther. 70 215-256 (1996)
  6. Advances in methods for atomic resolution macromolecular structure determination. Thompson MC, Yeates TO, Rodriguez JA. F1000Res 9 (2020)

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  1. Watching DNA polymerase η make a phosphodiester bond. Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W. Nature 487 196-201 (2012)
  2. Solvent dependence of dynamic transitions in protein solutions. Réat V, Dunn R, Ferrand M, Finney JL, Daniel RM, Smith JC. Proc. Natl. Acad. Sci. U.S.A. 97 9961-9966 (2000)
  3. Functional characteristics of the oxyanion hole in human acetylcholinesterase. Ordentlich A, Barak D, Kronman C, Ariel N, Segall Y, Velan B, Shafferman A. J. Biol. Chem. 273 19509-19517 (1998)
  4. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Radisky ES, Lee JM, Lu CJ, Koshland DE. Proc. Natl. Acad. Sci. U.S.A. 103 6835-6840 (2006)
  5. Assigning secondary structure from protein coordinate data. King SM, Johnson WC. Proteins 35 313-320 (1999)
  6. Neutron frequency windows and the protein dynamical transition. Becker T, Hayward JA, Finney JL, Daniel RM, Smith JC. Biophys. J. 87 1436-1444 (2004)
  7. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Hayward JA, Smith JC. Biophys. J. 82 1216-1225 (2002)
  8. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. PLoS Biol. 4 e99 (2006)
  9. Enzymology below 200 K: the kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase. Heyes DJ, Ruban AV, Wilks HM, Hunter CN. Proc. Natl. Acad. Sci. U.S.A. 99 11145-11150 (2002)
  10. Structure of a serine protease poised to resynthesize a peptide bond. Zakharova E, Horvath MP, Goldenberg DP. Proc. Natl. Acad. Sci. U.S.A. 106 11034-11039 (2009)
  11. Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Becker T, Smith JC. Phys Rev E Stat Nonlin Soft Matter Phys 67 021904 (2003)
  12. Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase. Wilmouth RC, Clifton IJ, Robinson CV, Roach PL, Aplin RT, Westwood NJ, Hajdu J, Schofield CJ. Nat. Struct. Biol. 4 456-462 (1997)
  13. Letter Trapping and visualization of a covalent enzyme-phosphate intermediate. Murphy JE, Stec B, Ma L, Kantrowitz ER. Nat. Struct. Biol. 4 618-622 (1997)
  14. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomès R, Prosser RS, Pai EF. Science 355 (2017)
  15. Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Ota N, Agard DA. Protein Sci. 10 1403-1414 (2001)
  16. Which properties of a spanning network of hydration water enable biological functions? Brovchenko I, Oleinikova A. Chemphyschem 9 2695-2702 (2008)
  17. Helix-enhancing propensity of fluoro and alkyl alcohols: influence of pH, temperature and cosolvent concentration on the helical conformation of peptides. Kumaran S, Roy RP. J. Pept. Res. 53 284-293 (1999)
  18. Unexpected active-site flexibility in the structure of human neutrophil elastase in complex with a new dihydropyrimidone inhibitor. Hansen G, Gielen-Haertwig H, Reinemer P, Schomburg D, Harrenga A, Niefind K. J. Mol. Biol. 409 681-691 (2011)
  19. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Hayward JA, Finney JL, Daniel RM, Smith JC. Biophys. J. 85 679-685 (2003)
  20. Visualizing phosphodiester-bond hydrolysis by an endonuclease. Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G. Nat. Struct. Mol. Biol. 22 65-72 (2015)
  21. Properties of the His57-Asp102 dyad of rat trypsin D189S in the zymogen, activated enzyme, and alpha1-proteinase inhibitor complexed forms. Kaslik G, Westler WM, Gráf L, Markley JL. Arch. Biochem. Biophys. 362 254-264 (1999)
  22. Conversion of trypsin to a functional threonine protease. Baird TT, Wright WD, Craik CS. Protein Sci. 15 1229-1238 (2006)
  23. Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastases, at 1.6 A resolution. Nakanishi I, Kinoshita T, Sato A, Tada T. Biopolymers 53 434-445 (2000)
  24. Combining Laue diffraction and molecular dynamics to study enzyme intermediates. Stoddard BL, Dean A, Bash PA. Nat. Struct. Biol. 3 590-595 (1996)
  25. New structural insights into the inhibition of serine proteases by cyclic peptides from bacteria. McDonough MA, Schofield CJ. Chem. Biol. 10 898-900 (2003)
  26. Crystal structure of a viral protease intramolecular acyl-enzyme complex: insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus. Chung IY, Paetzel M. J. Biol. Chem. 286 12475-12482 (2011)
  27. Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. Weik M, Vernede X, Royant A, Bourgeois D. Biophys. J. 86 3176-3185 (2004)
  28. Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants. Gokey T, Baird TT, Guliaev AB. J Mol Model 18 4941-4954 (2012)
  29. Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics. Ding X, Rasmussen BF, Petsko GA, Ringe D. Bioorg. Chem. 34 410-423 (2006)
  30. Universal dynamical onset in water at distinct material interfaces. Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Chem Sci 13 4341-4351 (2022)


Related citations provided by authors (1)

  1. Structure of Native Procine Pancreatic Elastase at 1.65 Angstroms Resolution. Meyer E, Cole G, Radhakrishnan R, Epp O Acta Crystallogr., B 44 26- (1988)

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