Catalytic Mechanisms of Heme Peroxidases

2010 ◽  
pp. 79-107 ◽  
Author(s):  
Paul R. Ortiz de Montellano
Keyword(s):  
Catalytic Mechanisms ◽  
Heme Peroxidases

scholarly journals Functional dissection of the catalytic mechanism of mammalian RNA polymerase II

2005 ◽  
Vol 83 (4) ◽  
pp. 497-504 ◽  
Author(s):  
Benoit Coulombe ◽  
Marie-France Langelier
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Catalytic Mechanism ◽  
Mutational Analysis ◽  
Structural Elements ◽  
Catalytic Mechanisms ◽  
Rnap Ii ◽  
Affinity Peptide

High resolution X-ray crystal structures of multisubunit RNA polymerases (RNAP) have contributed to our understanding of transcriptional mechanisms. They also provided a powerful guide for the design of experiments aimed at further characterizing the molecular stages of the transcription reaction. Our laboratory used tandem-affinity peptide purification in native conditions to isolate human RNAP II variants that had site-specific mutations in structural elements located strategically within the enzyme's catalytic center. Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme.Key words: RNA polymerase II, transcriptional mechanisms, mutational analysis, mRNA synthesis.

scholarly journals Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhiwen Liu ◽  
Fanglong Zhao ◽  
Boyang Zhao ◽  
Jie Yang ◽  
Joseph Ferrara ◽  
...  
Keyword(s):  
High Resolution ◽  
Organic Synthesis ◽  
Indole Alkaloids ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Computational Studies ◽  
X Ray ◽  
Evolutionary Branch ◽  
Catalytic Mechanisms

AbstractPrenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

scholarly journals Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29

2018 ◽  
Vol 293 (47) ◽  
pp. 18296-18308 ◽  
Author(s):  
Chelsea Vickers ◽  
Feng Liu ◽  
Kento Abe ◽  
Orly Salama-Alber ◽  
Meredith Jenkins ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Biological Activities ◽  
Bacterial Species ◽  
Structural Data ◽  
Side Chain ◽  
Glycoside Hydrolase Family ◽  
X Ray Crystallography ◽  
Catalytic Mechanisms ◽  
Thickening Agents ◽  
Hydrolase Family

Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas. Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.

scholarly journals Catalytic Elimination of Carbon Monoxide, Ethyl Acetate, and Toluene over the Ni/OMS-2 Catalysts

Catalysts ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 581
Author(s):  
Ning Dong ◽  
Mengyue Chen ◽  
Qing Ye ◽  
Dan Zhang ◽  
Hongxing Dai
Keyword(s):  
Ethyl Acetate ◽  
Molecular Sieve ◽  
Space Velocity ◽  
Oxidation Of Co ◽  
Toluene Oxidation ◽  
Catalytic Activities ◽  
Catalytic Mechanisms ◽  
Ni Species ◽  
Synthesized Materials ◽  
Incorporation Method

The Ni-loaded cryptomelane-type manganese oxide octahedral molecular sieve (OMS-2) catalysts (xNi/OMS-2: x = 1, 3, 5, and 10 wt%) were prepared by a pre-incorporation method. Physicochemical properties of the as-synthesized materials were characterized by means of various techniques, and their catalytic activities for CO, ethyl acetate, and toluene oxidation were evaluated.The loading of Ni played an important role in improving physicochemical propertiesof OMS-2. Among all of the samples, 5Ni/OMS-2 exhibited the best catalytic activity, with the T90 being 155 °C for CO oxidation at a space velocity (SV) of 60,000 mL/(g·h), 225°C for ethyl acetate oxidation at an SV of 240,000 mL/(g·h), and 300 °C for toluene oxidation at an SV of 240,000 mL/(g·h), which was due to its high Mn3+ content and Oads concentration, good low-temperature reducibility and lattice oxygen mobility, and strong interaction between the Ni species and the OMS-2 support. In addition, catalytic mechanisms of the oxidation of three pollutants over 5Ni/OMS-2 were also studied. The oxidation of CO, ethyl acetate, and toluene over the catalysts took place first via the activated adsorption, then intermediates formation, and finally complete conversion of the formed intermediates to CO2 and H2O.

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