scholarly journals Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanism Variants and Reaction Steps

2021 ◽  
Author(s):  
Paweł Kędzierski ◽  
Martyna Moskal ◽  
W. Andrzej Sokalski
Keyword(s):  
Reaction Mechanism ◽  
Enzyme Reaction ◽  
Catalytic Fields

Kinetics and Reaction Mechanism of the Carbamylphosphate Synthetase of a Multienzyme Aggregate from Yeast

1975 ◽  
Vol 53 (6) ◽  
pp. 721-730 ◽  
Author(s):  
David M. Aitken ◽  
Peter F. Lue ◽  
J. Gordin Kaplan
Keyword(s):  
Reaction Mechanism ◽  
Feedback Inhibition ◽  
Enzyme Reaction ◽  
Competitive Inhibitor ◽  
Potassium Ions ◽  
Ammonium Ions ◽  
Nitrogen Donor ◽  
Sequential Addition ◽  
A Site ◽  
Carbamylphosphate Synthetase

We have studied the kinetics and reaction mechanism of the carbamylphosphate synthetase of an enzyme aggregate functioning in the pyrimidine pathway of yeast. Mg–ATP was found to be one of the substrates of the enzyme reaction which was activated by free Mg2+ and inhibited by free ATP. Feedback inhibition by UTP was non-competitive with respect to both glutamine and bicarbonate. Potassium ions were essential for activity and could not be replaced by sodium. Glutamine could be replaced partially by ammonium ions as nitrogen donor. A bicarbonate-dependent cleavage of ATP was shown to take place in the absence of L-glutamine; L-glutamate was a competitive inhibitor of L-glutamine and the enzyme was shown to synthesize ATP when incubated with ADP and carbamyl phosphate. The reaction mechanism was found to involve sequential addition of the substrates bicarbonate and Mg–ATP and release of ADP, followed by addition of the third substrate glutamine. The purine nucleotide XMP had a pronounced activating effect on the enzyme, acting at a site different from that of UTP. Saturating levels of Mg–ATP eliminated this activation.

scholarly journals Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

2005 ◽  
pp. 5873 ◽  
Author(s):  
Silvia Ferrer ◽  
Estanislao Silla ◽  
Iñaki Tuñón ◽  
Mónica Oliva ◽  
Vicent Moliner ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Lactate Dehydrogenase ◽  
Enzyme Reaction ◽  
Protonation State

scholarly journals With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase

2014 ◽  
Author(s):  
Pedro J Silva
Keyword(s):  
Reaction Mechanism ◽  
Electron Donor ◽  
Ph Dependence ◽  
Single Point ◽  
Enzyme Reaction ◽  
Single Electron ◽  
Simple Explanation ◽  
Dependent Manner ◽  
Protochlorophyllide Oxidoreductase ◽  
Sequence Of Events

The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe-4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)// B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe-4S], yielding a negatively-charged intermediate. Depending on the rate of Fe-S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe-S cluster re-reduction should be the rate-limiting stage of the process. Poisson-Boltzmann computations on the full enzyme-substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe-S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjunction with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.

An Essential Role for Water in an Enzyme Reaction Mechanism:  The Crystal Structure of the Thymidylate Synthase Mutant E58Q†,‡

Biochemistry ◽  
1996 ◽  
Vol 35 (50) ◽  
pp. 16270-16281 ◽  
Author(s):  
Carleton R. Sage ◽  
Earl E. Rutenber ◽  
Thomas J. Stout ◽  
Robert M. Stroud
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Thymidylate Synthase ◽  
Essential Role ◽  
Enzyme Reaction

Atomic structure of theSerratia marcescensendonuclease at 1.1 Å resolution and the enzyme reaction mechanism

2000 ◽  
Vol 56 (5) ◽  
pp. 567-572 ◽  
Author(s):  
S. V. Shlyapnikov ◽  
V. V. Lunin ◽  
M. Perbandt ◽  
K. M. Polyakov ◽  
V. Yu. Lunin ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Atomic Structure ◽  
Enzyme Reaction

Simulation of the Enzyme Reaction Mechanism of Malate Dehydrogenase†

Biochemistry ◽  
1997 ◽  
Vol 36 (16) ◽  
pp. 4800-4816 ◽  
Author(s):  
Mark A. Cunningham ◽  
L. Lawrence Ho ◽  
Dzung T. Nguyen ◽  
Richard E. Gillilan ◽  
Paul A. Bash
Keyword(s):  
Reaction Mechanism ◽  
Malate Dehydrogenase ◽  
Enzyme Reaction
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