Interaction of Inhibitors with Phosphoenolpyruvate Mutase: Implications for the Reaction Mechanism and the Nature of the Active Site

Biochemistry ◽  
1994 ◽  
Vol 33 (18) ◽  
pp. 5641-5646 ◽  
Author(s):  
H. Martin Seidel ◽  
Jeremy R. Knowles
Keyword(s):  
Reaction Mechanism ◽  
Active Site ◽  
Phosphoenolpyruvate Mutase

The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

2014 ◽  
Vol 70 (12) ◽  
pp. 3212-3225 ◽  
Author(s):  
Tiila-Riikka Kiema ◽  
Rajesh K. Harijan ◽  
Malgorzata Strozyk ◽  
Toshiyuki Fukao ◽  
Stefan E. H. Alexson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Active Site ◽  
Quaternary Structure ◽  
Fatty Acyl ◽  
Physiological Importance ◽  
Loop Domain ◽  
Solution Studies ◽  
Hydrolysis Of ◽  
Insight Into

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

scholarly journals Reaction Mechanism of the ε Subunit ofE. coliDNA Polymerase III: Insights into Active Site Metal Coordination and Catalytically Significant Residues

2009 ◽  
Vol 131 (4) ◽  
pp. 1550-1556 ◽  
Author(s):  
G. Andrés Cisneros ◽  
Lalith Perera ◽  
Roel M. Schaaper ◽  
Lars C. Pedersen ◽  
Robert E. London ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Active Site ◽  
Metal Coordination ◽  
Polymerase Iii

scholarly journals Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45)

2017 ◽  
Vol 15 (30) ◽  
pp. 6310-6313 ◽  
Author(s):  
Alexander G. Ekström ◽  
Van Kelly ◽  
Jon Marles-Wright ◽  
Scott L. Cockroft ◽  
Dominic J. Campopiano
Keyword(s):  
Mass Spectrometry ◽  
Reaction Mechanism ◽  
Active Site ◽  
Covalent Modification ◽  
Elimination Reaction ◽  
Covalent Adduct ◽  
Michael Type Addition

Mass spectrometry and modelling shows the antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael type addition elimination reaction mechanism.

scholarly journals Proton–Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

2020 ◽  
Vol 142 (23) ◽  
pp. 10412-10423 ◽  
Author(s):  
Daniel Bím ◽  
Jakub Chalupský ◽  
Martin Culka ◽  
Edward I. Solomon ◽  
Lubomír Rulíšek ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Reaction Mechanism ◽  
Active Site ◽  
Δ9 Desaturase

Insight into the active site and reaction mechanism for selective oxidation of methane to methanol using H2O2 on a Rh1/ZrO2 catalyst

2020 ◽  
Vol 44 (4) ◽  
pp. 1632-1639 ◽  
Author(s):  
Qi Zhao ◽  
Bing Liu ◽  
Yuebing Xu ◽  
Feng Jiang ◽  
Xiaohao Liu
Keyword(s):  
Reaction Mechanism ◽  
Selective Oxidation ◽  
Active Site ◽  
Oxidation Of Methane ◽  
Methanol Formation ◽  
Zro2 Catalyst ◽  
Insight Into

Five-coordinated Rh leads to the over-oxidation of CH4, while four-coordinated Rh stabilizes CH3 and facilitates methanol formation via the CH3OOH intermediate.

scholarly journals The metal centres of particulate methane mono-oxygenase

2008 ◽  
Vol 36 (6) ◽  
pp. 1134-1137 ◽  
Author(s):  
Amy C. Rosenzweig
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Structure Determination ◽  
Active Site ◽  
Spectroscopic Data ◽  
Present Review ◽  
Methylococcus Capsulatus ◽  
Research Groups ◽  
Oxidation Of Methane ◽  
Before And After

pMMO (particulate methane mono-oxygenase) is an integral membrane metalloenzyme that catalyses the oxidation of methane to methanol. The pMMO metal active site has not been identified, precluding detailed investigation of the reaction mechanism. Models for the metal centres proposed by various research groups have evolved as crystallographic and spectroscopic data have become available. The present review traces the evolution of these active-site models before and after the 2005 Methylococcus capsulatus (Bath) pMMO crystal structure determination.

scholarly journals Bicarbonate-dependent ATP cleavage catalysed by pyruvate carboxylase in the absence of pyruvate

1992 ◽  
Vol 287 (3) ◽  
pp. 1011-1017 ◽  
Author(s):  
P V Attwood ◽  
B D L A Graneri
Keyword(s):  
Reaction Mechanism ◽  
Atpase Activity ◽  
Active Site ◽  
Pyruvate Carboxylase ◽  
Substrate Inhibition ◽  
Cleavage Reaction ◽  
Acetyl Coa ◽  
Enzyme Preparations ◽  
Pyruvate Carboxylation ◽  
Rate Of Movement

Preparations of pyruvate carboxylase catalyse the cleavage of MgATP in the absence of pyruvate and acetyl-CoA. The rate of this cleavage is higher in the presence of HCO3- than in its absence. Incubation of the enzyme preparations with an excess of the pyruvate carboxylase inhibitor, avidin, completely abolishes the pyruvate carboxylating activity of the enzyme preparations but only abolishes the HCO3(-)-dependent MgATP cleaving activity, with no effect on the HCO3(-)-independent ATPase activity. The HCO3(-)-dependent MgATP cleavage is also sensitive to inhibition by a pyruvate carboxylase inhibitor, oxamate, and the dependence of the reaction on the free Mg2+ concentration is similar to that of the pyruvate-carboxylation reaction, whereas the HCO3(-)-independent MgATP cleavage is not dependent on the concentration of free Mg2+ in the range tested. This indicates that MgATP cleavage by pyruvate carboxylase is entirely dependent on the presence of HCO3- and that there may be a low level of ATPase contamination in the enzyme preparations. In addition, inhibition of the HCO3(-)-dependent MgATP cleavage by both avidin and oxamate indicate that although biotin does not directly participate in the reaction, its presence is required in that part of the active site of the enzyme. The rate of HCO3(-)-dependent MgATP cleavage is about 0.07% of that of the full pyruvate carboxylation reaction under similar conditions with saturating substrates. The reaction mechanism is sequential with respect to MgATP and HCO3- addition and Mg2+ adds at equilibrium before MgATP. Acetyl-CoA stimulates the HCO3(-)-dependent MgATP cleavage at low MgATP concentrations, with the stimulation being greater at low Mg2+ concentrations. At high levels of MgATP in the presence of acetyl-CoA, substrate inhibition is evident and is more pronounced at increasing concentrations of Mg2+. This inhibition appears to be, at least in part, caused by inhibition of decarboxylation of the enzyme-carboxybiotin complex by the binding to this complex of Mg2+ and MgATP, which probably act to reduce the rate of movement of carboxybiotin from the site of the MgATP cleavage reaction to that of the pyruvate carboxylation reaction where it is unstable and decarboxylates.

In situ and operando analysis of environmental catalysts – studies on reaction mechanism and active site

Catalysis ◽  
2019 ◽  
pp. 242-266
Author(s):  
Kazumasa Murata ◽  
Kakuya Ueda ◽  
Yuji Mahara ◽  
Junya Ohyama ◽  
Atsushi Satsuma
Keyword(s):  
Reaction Mechanism ◽  
Active Site ◽  
Environmental Catalysts

Nitrogen and Sulfur Transferases

2007 ◽  
Author(s):  
Perry A. Frey ◽  
Adrian D. Hegeman
Keyword(s):  
Steady State ◽  
Reaction Mechanism ◽  
Active Site ◽  
Reaction Mechanisms ◽  
Radical Reaction ◽  
Amino Group ◽  
Steady State Kinetics ◽  
Ping Pong ◽  
Polar Reaction

Unlike other group transfer reactions in biochemistry, the actions of nitrogen transferring enzymes do not follow a single unifying chemical principle. Nitrogen-transferring enzymes catalyze aminotransfer, amidotransfer, and amidinotransfer. An aminotransferase catalyzes the transfer of the NH2 group from a primary amine to a ketone or aldehyde. An amidotransferase catalyzes the transfer of the anide-NH2 group from glutamine to another group. These reactions proceed by polar reaction mechanisms. Aminomutases catalyze 1,2-intramolecular aminotransfer, in which an amino group is inserted into an adjacent C—H bond. The action of lysine 2,3-aminomutase, described in chapter 7, is an example of an aminomutase that functions by a radical reaction mechanism. Tyrosine 2,3-aminomutase also catalyzes the 2,3-amino migration, but it does so by a polar reaction mechanism. In this chapter, we consider NH2-transferring enzymes that function by polar reaction mechanisms. Transaminases or aminotransferases are the most extensively studied pyridoxal-5'-phosphate (PLP)–dependent enzymes, and many aminotransferases catalyze essential steps in catabolic and anabolic metabolism. In the classic transaminase reaction, aspartate aminotransferase (AAT) catalyzes the fully reversible reaction of L-aspartate with α-ketoglutarate according to fig. 13-1 to form oxaloacetate and L-glutamate. Like all aminotransferases, AAT is PLP dependent, and PLP functions in its classic role of providing a reactive carbonyl group to function in facilitating the cleavage of the α-H of aspartate and the departure of the α-amino group of aspartate for transfer to α-ketoglutarate (Snell, 1962). PLP in the holoenzyme functions in essence to stabilize the α-carbanions of L-aspartate or L-glutamate, the major biological role of PLP discussed in chapter 3. The functional groups of the enzyme catalyze steps in the mechanism, such as the 1,3-prototropic shift of the α-proton to C4' of pyridoxamine 5'-phosphate (PMP). The steady-state kinetics corresponds to the ping pong bi bi mechanism shown at the bottom of fig. 13-1. This mechanism allows L-aspartate to react with the internal aldimine, E=PLP in fig. 13-1, to produce an equivalent of oxaloacetate, with conversion of PLP to PMP at the active site (E.PMP), the free, covalently modified enzyme in the ping pong mechanism.

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