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Titolo:
Yeast chorismate mutase in the R state: Simulations of the active site
Autore:
Ma, JP; Zheng, XF; Schnappauf, G; Braus, G; Karplus, M; Lipscomb, WN;
Indirizzi:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard UnivCambridge MA USA 02138 & Chem Biol, Cambridge, MA 02138 USA Univ Gottingen, Inst Mikrobiol & Genet, D-37077 Gottingen, Germany Univ Gottingen Gottingen Germany D-37077 net, D-37077 Gottingen, Germany UniveStrasbourg 1, Inst Le Bel, Lab Chim Biophys, F-67000 Strasbourg, Franc Univ Strasbourg 1 Strasbourg France F-67000 s, F-67000 Strasbourg, Franc
Titolo Testata:
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
fascicolo: 25, volume: 95, anno: 1998,
pagine: 14640 - 14645
SICI:
0027-8424(199812)95:25<14640:YCMITR>2.0.ZU;2-E
Fonte:
ISI
Lingua:
ENG
Soggetto:
MOLECULAR-FORCE FIELD; TRANSITION-STATE; BACILLUS-SUBTILIS; CRYSTAL-STRUCTURES; PREPHENATE; MECHANISM; DYNAMICS; ENZYME; MMFF94; REARRANGEMENT;
Keywords:
allosteric enzyme; molecular dynamics; stochastic boundary condition; enzyme catalysis; protonation state;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
42
Recensione:
Indirizzi per estratti:
Indirizzo: Lipscomb, WN Harvard Univ, Dept Chem & Chem Biol, 12 Oxford St, Cambridge,MA 02138 USA Harvard Univ 12 Oxford St Cambridge MA USA 02138 MA 02138 USA
Citazione:
J.P. Ma et al., "Yeast chorismate mutase in the R state: Simulations of the active site", P NAS US, 95(25), 1998, pp. 14640-14645

Abstract

The isomerization of chorismate to prephenate by chorismate mutase in the biosynthetic pathway that forms Tyr and Phe involves C5-O (ether) bond cleavage and C1-C9 bond formation in a Claisen rearrangement. Development of negative charge on the ether oxygen, stabilized by Lys-168 and Glu-246, is inferred from the structure of a complex with a transition state analogue (TSA) and from the pH-rate profile of the enzyme and the E246Q mutant. These studies imply a protonated Glu-246 well above pH 7. Here, several 500-ps molecular dynamics simulations test the stability of enzyme-TSA. complexes by using a solvated system with stochastic boundary conditions. The simulated systems are (i) protonated Glu-246 (stable), (ii) deprotonated Glu-246 (unstable), (iii) deprotonated Glu-246 plus one H2O between Glu-246 and the ether oxygen (unstable), (iv) the E246Q mutant (stable), and (nu) addition of OH- between protonated Glu-246 and the ether oxygen. In (nu), a local conformational change of Lys-168 displaced the OH- into the solvent region, suggesting a possible rate-determining step that precedes the catalytic step. In a 500-ps simulation of the enzyme complexed with the reactant chorismate or the product prephenate, no water molecule remained near the oxygen of the ligand. Calculations using the linearized Poisson-Boltzmann equation showthat the effective pK(a) of Glu-246 is shifted from 5.8 to 8.1 as the negative charge on the ether oxygen of the TSA is changed from -0.56 electron to -0.9 electron. Altogether, these results support retention of a proton onGlu-246 to high pH and the absence of a water molecule in the catalytic steps.

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Documento generato il 16/07/20 alle ore 14:32:17