Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase†

Biochemistry ◽  
2003 ◽  
Vol 42 (7) ◽  
pp. 1820-1830 ◽  
Author(s):  
Elena S. Polovnikova ◽  
Michael J. McLeish ◽  
Eduard A. Sergienko ◽  
John T. Burgner ◽  
Natalie L. Anderson ◽  
...  
Keyword(s):  
Kinetic Analysis ◽  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

The Crystal Structure of Benzoylformate Decarboxylase at 1.6 Å Resolution:  Diversity of Catalytic Residues in Thiamin Diphosphate-Dependent Enzymes†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (28) ◽  
pp. 9918-9930 ◽  
Author(s):  
Miriam S. Hasson ◽  
Angelika Muscate ◽  
Michael J. McLeish ◽  
Lena S. Polovnikova ◽  
John A. Gerlt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thiamin Diphosphate ◽  
Catalytic Residues ◽  
Benzoylformate Decarboxylase

scholarly journals Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

2019 ◽  
Vol 15 ◽  
pp. 145-159 ◽  
Author(s):  
Ferran Planas ◽  
Michael J McLeish ◽  
Fahmi Himo
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Thiamin Diphosphate ◽  
Diverse Range ◽  
Factors Affecting ◽  
Benzoylformate Decarboxylase ◽  
Carbon Carbon Bond ◽  
Activated State ◽  
Catalyzed Reactions ◽  
The Individual

Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions. In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.

Mechanism-Based Inactivation of Benzoylformate Decarboxylase, A Thiamin Diphosphate-Dependent Enzyme

2007 ◽  
Vol 129 (14) ◽  
pp. 4120-4121 ◽  
Author(s):  
Asim K. Bera ◽  
Lena S. Polovnikova ◽  
Juliatek Roestamadji ◽  
Theodore S. Widlanski ◽  
George L. Kenyon ◽  
...  
Keyword(s):  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

Spectroscopic Detection of Transient Thiamin Diphosphate-Bound Intermediates on Benzoylformate Decarboxylase†

Biochemistry ◽  
2000 ◽  
Vol 39 (45) ◽  
pp. 13862-13869 ◽  
Author(s):  
Eduard A. Sergienko ◽  
Jue Wang ◽  
Lena Polovnikova ◽  
Miriam S. Hasson ◽  
Michael J. McLeish ◽  
...  
Keyword(s):  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

scholarly journals Detection and Time Course of Formation of Major Thiamin Diphosphate-Bound Covalent Intermediates Derived from a Chromophoric Substrate Analogue on Benzoylformate Decarboxylase†

Biochemistry ◽  
2009 ◽  
Vol 48 (5) ◽  
pp. 981-994 ◽  
Author(s):  
Sumit Chakraborty ◽  
Natalia S. Nemeria ◽  
Anand Balakrishnan ◽  
Gabriel S. Brandt ◽  
Malea M. Kneen ◽  
...  
Keyword(s):  
Time Course ◽  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase ◽  
Substrate Analogue

Kinetic Aspects of the Interaction of Blood Clotting Enzymes

1965 ◽  
Vol 13 (01) ◽  
pp. 155-175 ◽  
Author(s):  
H. C Hemker ◽  
P.W Hemker ◽  
E. A Loeliger
Keyword(s):  
Kinetic Analysis ◽  
Enzyme Kinetics ◽  
Blood Clotting ◽  
Enzyme System ◽  
Enzyme Kinetic ◽  
Clotting Time ◽  
Standard Methods

SummaryApplication of the methods of enzyme-kinetic analysis to the results of clotting tests is feasible and can yield useful results. However, the standard methods of enzyme kinetics are not applicable without modifications imposed by the peculiarities of the blood-clotting enzyme system. The influence of the following complicating circumstances is calculated :1. Substrate is not present in excess.2. Only relative measures exist for concentrations of substrate or enzymes.3. Enzymes and substrates are often added together.4. Reagents are not pure.5. Clotting-time is our only measure for clotting-velocity.Formulas are deduced, which makes it possible to recognize the effect of these complications.

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