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

Facile Metal Coordination of Active Site Imprinted Nitrogen Doped Carbons for the Conservative Preparation of Non-Noble Metal Oxygen Reduction Electrocatalysts

2017 ◽  
Vol 8 (9) ◽  
pp. 1701771 ◽  
Author(s):  
Asad Mehmood ◽  
Jonas Pampel ◽  
Ghulam Ali ◽  
Heung Yong Ha ◽  
Francisco Ruiz-Zepeda ◽  
...  
Keyword(s):  
Oxygen Reduction ◽  
Noble Metal ◽  
Active Site ◽  
Metal Coordination ◽  
Nitrogen Doped

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 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.

scholarly journals Structure of the θ Subunit of Escherichia coli DNA Polymerase III in Complex with the ε Subunit

2006 ◽  
Vol 188 (12) ◽  
pp. 4464-4473 ◽  
Author(s):  
Max A. Keniry ◽  
Ah Young Park ◽  
Elisabeth A. Owen ◽  
Samir M. Hamdan ◽  
Guido Pintacuda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Active Site ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Dna Polymerase Iii ◽  
Pseudocontact Shifts ◽  
Catalytic Core ◽  
Lanthanide Ion ◽  
Polymerase Iii

ABSTRACT The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the α, ε, and θ subunits. The θ subunit is the smallest and least understood subunit. The three-dimensional structure of θ in a complex with the unlabeled N-terminal domain of the ε subunit, ε186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of ε186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of θ in a methanol-water buffer and of the bacteriophage P1 homolog, HOT, in aqueous buffer. Conserved nuclear Overhauser enhancement (NOE) patterns obtained for free and complexed θ show that most of the structure changes little upon complex formation. Discrepancies with respect to a previously published structure of free θ (Keniry et al., Protein Sci. 9:721-733, 2000) were attributed to errors in the latter structure. The present structure satisfies the pseudocontact shifts better than either the structure of θ in methanol-water buffer or the structure of HOT. satisfies these shifts. The epitope of ε186 on θ was mapped by NOE difference spectroscopy and was found to involve helix 1 and the C-terminal part of helix 3. The pseudocontact shifts indicated that the helices of θ are located about 15 Å or farther from the lanthanide ion in the active site of ε186, in agreement with the extensive biochemical data for the θ-ε system.

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