Catalytic Mechanism of Scytalone Dehydratase:  Site-Directed Mutagenisis, Kinetic Isotope Effects, and Alternate Substrates

Biochemistry ◽  
1999 ◽  
Vol 38 (19) ◽  
pp. 6012-6024 ◽  
Author(s):  
Gregory S. Basarab ◽  
James J. Steffens ◽  
Zdzislaw Wawrzak ◽  
Rand S. Schwartz ◽  
Tomas Lundqvist ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope ◽  
Scytalone Dehydratase

scholarly journals Catalytic mechanism of a family 3 β-glucosidase and mutagenesis study on residue Asp-247

2001 ◽  
Vol 355 (3) ◽  
pp. 835-840 ◽  
Author(s):  
Yaw-Kuen LI ◽  
Jiunly CHIR ◽  
Fong-Yi CHEN
Keyword(s):  
Amino Acid ◽  
Essential Amino Acid ◽  
Catalytic Mechanism ◽  
Bond Cleavage ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Wild Type Enzyme ◽  
Kinetic Isotope

A family 3 β-glucosidase (EC 3.2.1.21) from Flavobacterium meningosepticum has been cloned and overexpressed. The mechanistic action of the enzyme was probed by NMR spectroscopy and kinetic investigations, including substrate reactivity, secondary kinetic isotope effects and inhibition studies. The stereochemistry of enzymic hydrolysis was identified as occurring with the retention of an anomeric configuration, indicating a double-displacement reaction. Based on the kcat values with a series of aryl glucosides, a Bronsted plot with a concave-downward shape was constructed. This biphasic behaviour is consistent with a two-step mechanism involving the formation and breakdown of a glucosyl–enzyme intermediate. The large Bronsted constant (β =-0.85) for the leaving-group-dependent portion (pKa of leaving phenols > 7) indicates substantial bond cleavage at the transition state. Secondary deuterium kinetic isotope effects with 2,4-dinitrophenyl β-D-glucopyanoside, o-nitrophenyl β-D-glucopyanoside and p-cyanophenyl β-D-glucopyanoside as substrates were 1.17±0.02, 1.19±0.02 and 1.04±0.02 respectively. These results support an SN1-like mechanism for the deglucosylation step and an SN2-like mechanism for the glucosylation step. Site-directed mutagenesis was also performed to study essential amino acid residues. The activities (kcat/Km) of the D247G and D247N mutants were 30000- and 200000-fold lower respectively than that of the wild-type enzyme, whereas the D247E mutant retained 20% of wild-type activity. These results indicate that Asp-247 is an essential amino acid. It is likely that this residue functions as a nucleophile in the reaction. This conclusion is supported by the kinetics of the irreversible inactivation of the wild-type enzyme by conduritol-B-epoxide, compared with the much slower inhibition of the D247E mutant and the lack of irreversible inhibition of the D247G mutant.

scholarly journals The catalytic mechanism of the Suzuki-Miyaura reaction

2021 ◽  
Author(s):  
Juliet macharia ◽  
Chetan Joshi ◽  
Joseph Izzo ◽  
Victor Wambua ◽  
Sungjin Kim ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Palladium Complex ◽  
Isotope Effects ◽  
Oxidative Addition ◽  
Kinetic Isotope Effects ◽  
Boronic Acids ◽  
Aryl Halides ◽  
Kinetic Isotope ◽  
Aryl Bromides ◽  
Insight Into

Abstract: Experimental and theoretical 13C kinetic isotope effects are utilized to obtain atomistic insight into the catalytic mechanism of the Pd(PPh3)4 catalyzed Suzuki-Miyaura reaction of aryl halides and aryl boronic acids. Under catalytic conditions, we establish that oxidative addition of aryl bromides occurs to a 12-electron monoligated palladium complex (Pd(PPh3)). For aryl iodides, the first irreversible step in the catalytic cycle precedes oxidative addition and is shown to be binding of the iodoarene to Pd(PPh3). Our results suggest that the commonly proposed oxidative addition to the 14-electron Pd(PPh3)2 complex can occur only in the presence of excess added ligand or under stoichiometric conditions. The transmetalation step, under catalytic conditions, is shown to proceed via a tetracoordinate boronate (8B4) intermediate with a Pd-O-B linkage.

Theoretical Simulations of Heavy-Atom Kinetic Isotope Effects in Aliphatic Claisen Rearrangement

2020 ◽  
Vol 124 (51) ◽  
pp. 10678-10686
Author(s):  
Yuqing Xu ◽  
Kin-Yiu Wong ◽  
Meishan Wang ◽  
Desheng Liu ◽  
Wenkai Zhao ◽  
...  
Keyword(s):  
Claisen Rearrangement ◽  
Isotope Effects ◽  
Heavy Atom ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope ◽  
Theoretical Simulations

Direct dynamics calculations of reaction rate and kinetic isotope effects in enzyme catalysed reactions

2002 ◽  
Vol 122 ◽  
pp. 223-242 ◽  
Author(s):  
Gary Tresadern ◽  
Sara Nunez ◽  
Paul F. Faulder ◽  
Hong Wang ◽  
Ian H. Hillier ◽  
...  
Keyword(s):  
Reaction Rate ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Direct Dynamics ◽  
Kinetic Isotope

Interpretation of Transient-State Kinetic Isotope Effects†

Biochemistry ◽  
1996 ◽  
Vol 35 (1) ◽  
pp. 83-88 ◽  
Author(s):  
Harvey F. Fisher ◽  
Swapan K. Saha
Keyword(s):  
Isotope Effects ◽  
Transient State ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope ◽  
State Kinetic
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