Why does tautomycetin thioesterase prefer hydrolysis to macrocyclization? Theoretical study on its catalytic mechanism

2019 ◽  
Vol 9 (22) ◽  
pp. 6391-6403
Author(s):  
Lei Liu ◽  
Wentao Tao ◽  
Linquan Bai ◽  
Eung-Soo Kim ◽  
Yi-Lei Zhao ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Catalytic Mechanism ◽  
Theoretical Study

In this study, we attempted to uncover the reasons why Tautomycetin thioesterase (TMC TE) prefers hydrolysis rather than macrocyclization, and reveal the molecular basis of TE-catalyzed hydrolysis and macrocyclization.

scholarly journals Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane

2015 ◽  
Vol 17 (28) ◽  
pp. 18653-18664 ◽  
Author(s):  
Pooria Farahani ◽  
Marcus Lundberg ◽  
Roland Lindh ◽  
Daniel Roca-Sanjuán
Keyword(s):  
Excited State ◽  
Molecular Basis ◽  
Theoretical Study ◽  
Chemical Processes ◽  
State Chemical

We report on the molecular basis of excited-state chemical processes that are induced by intramolecular chemiexcitation rather than by irradiation.

Catalytic Mechanism of Calcium on the Formation of HCN during Pyrolysis of Pyrrole and Indole: A Theoretical Study

2019 ◽  
Vol 33 (11) ◽  
pp. 11516-11523 ◽  
Author(s):  
Ji Liu ◽  
Xin-rui Fan ◽  
Wei Zhao ◽  
Bin Hu ◽  
Ding-jia Liu ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Theoretical Study

Catalytic Mechanism of Glyoxalase I:  A Theoretical Study

2001 ◽  
Vol 123 (42) ◽  
pp. 10280-10289 ◽  
Author(s):  
Fahmi Himo ◽  
Per E. M. Siegbahn
Keyword(s):  
Catalytic Mechanism ◽  
Theoretical Study ◽  
Glyoxalase I

Insights into the binding specificity and catalytic mechanism ofN-acetylhexosamine 1-phosphate kinases through multiple reaction complexes

2014 ◽  
Vol 70 (5) ◽  
pp. 1401-1410 ◽  
Author(s):  
Kuei-Chen Wang ◽  
Syue-Yi Lyu ◽  
Yu-Chen Liu ◽  
Chin-Yuan Chang ◽  
Chang-Jer Wu ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Bifidobacterium Longum ◽  
Three Dimensional ◽  
Binding Specificity ◽  
Chemoenzymatic Synthesis ◽  
Leloir Pathway ◽  
The Given

Utilization ofN-acetylhexosamine in bifidobacteria requires the specific lacto-N-biose/galacto-N-biose pathway, a pathway differing from the Leloir pathway while establishing symbiosis between humans and bifidobacteria. The genelnpBin the pathway encodes a novel hexosamine kinase NahK, which catalyzes the formation ofN-acetylhexosamine 1-phosphate (GlcNAc-1P/GalNAc-1P). In this report, seven three-dimensional structures of NahK in complex with GlcNAc, GalNAc, GlcNAc-1P, GlcNAc/AMPPNP and GlcNAc-1P/ADP from bothBifidobacterium longum(JCM1217) andB. infantis(ATCC15697) were solved at resolutions of 1.5–2.2 Å. NahK is a monomer in solution, and its polypeptide folds in a crescent-like architecture subdivided into two domains by a deep cleft. The NahK structures presented here represent the first multiple reaction complexes of the enzyme. This structural information reveals the molecular basis for the recognition of the given substrates and products, GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg2+, and provides insights into the catalytic mechanism, enabling NahK and mutants thereof to form a choice of biocatalysts for enzymatic and chemoenzymatic synthesis of carbohydrates.

scholarly journals Theoretical study of catalytic mechanism for single-site water oxidation process

2012 ◽  
Vol 109 (39) ◽  
pp. 15669-15672 ◽  
Author(s):  
X. Lin ◽  
X. Hu ◽  
J. J. Concepcion ◽  
Z. Chen ◽  
S. Liu ◽  
...  
Keyword(s):  
Water Oxidation ◽  
Catalytic Mechanism ◽  
Theoretical Study ◽  
Oxidation Process ◽  
Single Site ◽  
Site Water

A Theoretical Study of the Catalytic Mechanism of Formate Dehydrogenase

2008 ◽  
Vol 112 (32) ◽  
pp. 10012-10022 ◽  
Author(s):  
R. Castillo ◽  
M. Oliva ◽  
S. Martí ◽  
V. Moliner
Keyword(s):  
Formate Dehydrogenase ◽  
Catalytic Mechanism ◽  
Theoretical Study

scholarly journals Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates

2019 ◽  
Vol 116 (8) ◽  
pp. 2919-2924 ◽  
Author(s):  
Xiao Zhang ◽  
Lian-Huan Wei ◽  
Yuxin Wang ◽  
Yu Xiao ◽  
Jun Liu ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Catalytic Mechanism ◽  
Tertiary Structure ◽  
Structural Basis ◽  
Multiple Substrates ◽  
Functional Studies ◽  
Structural Insights ◽  
Demethylation Activity

FTO demethylates internal N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am; at the cap +1 position) in mRNA, m6A and m6Am in snRNA, and N1-methyladenosine (m1A) in tRNA in vivo, and in vitro evidence supports that it can also demethylate N6-methyldeoxyadenosine (6mA), 3-methylthymine (3mT), and 3-methyluracil (m3U). However, it remains unclear how FTO variously recognizes and catalyzes these diverse substrates. Here we demonstrate—in vitro and in vivo—that FTO has extensive demethylation enzymatic activity on both internal m6A and cap m6Am. Considering that 6mA, m6A, and m6Am all share the same nucleobase, we present a crystal structure of human FTO bound to 6mA-modified ssDNA, revealing the molecular basis of the catalytic demethylation of FTO toward multiple RNA substrates. We discovered that (i) N6-methyladenine is the most favorable nucleobase substrate of FTO, (ii) FTO displays the same demethylation activity toward internal m6A and m6Am in the same RNA sequence, suggesting that the substrate specificity of FTO primarily results from the interaction of residues in the catalytic pocket with the nucleobase (rather than the ribose ring), and (iii) the sequence and the tertiary structure of RNA can affect the catalytic activity of FTO. Our findings provide a structural basis for understanding the catalytic mechanism through which FTO demethylates its multiple substrates and pave the way forward for the structure-guided design of selective chemicals for functional studies and potential therapeutic applications.

Quantum chemistry study on the oxidation of NO catalyzed by ZSM5 supported Mn/Co–Al/Ce

2017 ◽  
Vol 16 (05) ◽  
pp. 1750044 ◽  
Author(s):  
Zhengcheng Wen ◽  
Mengmeng Du ◽  
Yuan Li ◽  
Zhihua Wang ◽  
Jiangrong Xu ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Catalytic Effect ◽  
Catalytic Mechanism ◽  
Theoretical Study ◽  
No Oxidation ◽  
Quantum Chemistry Calculation ◽  
Detailed Mechanism ◽  
Chemistry Calculation ◽  
Oxidation Of No ◽  
Theoretical Results

The detailed mechanism of NO oxidation catalyzed by ZSM5 supported Mn/Co–Al/Ce is investigated and revealed by Quantum Chemistry Calculation. A three-step catalytic mechanism for NO oxidation is proposed and studied. Theoretical results show that, the activate energies of reactions catalyzed by ZSM-5 supported Mn/Co (71.1[Formula: see text]kJ/mol/80.6[Formula: see text]kJ/mol) are much lower than that obtained from the direct NO oxidation. This indicates that the ZSM-5 supported Mn/Co has an obvious catalytic effect. When the active center Si is replaced by Al and Ce, the activation energies are further decreased to about 40[Formula: see text]kJ/mol. This indicates that the doping of Al and Ce can obviously improve the catalytic effect. The theoretical study illustrates that the catalysts for NO oxidation not only relate to the supported transition metal such as Co and Mn, but also highly relate to the activity centers such as Al and Ce.

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