scholarly journals Multi-active Site Dynamics on a Molecular Cr/Co/Se Cluster Catalyst

2022 ◽  
Author(s):  
Jonathan Kephart ◽  
Benjamin Mitchell ◽  
Werner Kaminsky ◽  
Alexandra Velian
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Resting State ◽  
Active Sites ◽  
Stepwise Mechanism ◽  
Nitrene Transfer ◽  
Catalytic Intermediates ◽  
Edge Site ◽  
Catalytically Active

This study provides detailed insights into the interconnected reactivity of the three catalytically active sites of an atomically precise nanocluster Cr3(py)3Co6Se8L6 (Cr3(py)3, L = Ph2PNTol–, Ph = phenyl, Tol = 4-tolyl). Catalytic and stoichiometric studies into tosyl azide activation and carbodiimide formation enabled the isolation and crystallographic characterization of key metal-nitrenoid catalytic intermediates, including the tris(nitrenoid) cluster Cr3(NTs)3, the catalytic resting state Cr3(NTs)3(CNtBu)3, and the mono(nitrenoid) cluster Cr3(NTs)(CNtBu)2. Nitrene transfer proceeds via a stepwise mechanism, with the three active sites engaging sequentially to produce carbodiimide. Comparative structural analysis and CNtBu bind-ing studies reveal that the chemical state of neighboring active sites regulates the affinity for substrates of an individual Cr-nitrenoid edge site, intertwining their reactivity through the inorganic support.

scholarly journals The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5053
Author(s):  
Alina K. Bakunova ◽  
Alena Yu. Nikolaeva ◽  
Tatiana V. Rakitina ◽  
Tatiana Y. Isaikina ◽  
Maria G. Khrenova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structural Analysis ◽  
Active Site ◽  
Active Sites ◽  
Structural Basis ◽  
Active Site Residues ◽  
Type Iv ◽  
Fold Type ◽  
Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

scholarly journals Characterization and Structure Elucidation of Binary Zr:Ti MEL Structure; Simultaneous Photodegradation/Removal of Organic–Inorganic Pollutants

Catalysts ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 633
Author(s):  
Samia A. Kosa ◽  
Islam H. Abd El Maksod ◽  
Eman Z. Hegazy ◽  
Naha M. Al-sebaii
Keyword(s):  
Crystalline Phase ◽  
Active Site ◽  
Structure Elucidation ◽  
Active Sites ◽  
Mutual Effect ◽  
Blue Dye ◽  
Inorganic Pollutants ◽  
Full Characterization ◽  
Cobalt And Nickel

The preparation of a series of different Ti/Zr MEL structure was performed successfully. Full characterization of the prepared materials was done using XRD, IR, DR, and SEM. The results show that the prepared materials contain only one crystalline phase (ZSM-11). The affinity of Zr to form the crystalline phase alone in a binary Zr/Ti synthesizing mixture was approved by SEM and elemental analysis results. The percentage of each active site was calculated. DR spectra were deconvoluted, and three active sites were supposed and quantified (tetragonal, octahedral, and crystalline). The mutual effect of ions (lead, copper, cobalt, and nickel) and methylene blue dye on the removal efficiency with and without ultraviolet irradiation was examined and fully characterized. The ions largely influence the photodegradation process, and a mechanism was formulated. Meanwhile, the presence of dye showed a negligible effect on the removal of ions.

scholarly journals A Unique Ru-N4-P Coordinated Structure Synergistically Waking Up the Nonmetal P Active Site for Hydrogen Production

Research ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Chuanqiang Wu ◽  
Shiqing Ding ◽  
Daobin Liu ◽  
Dongdong Li ◽  
Shuangming Chen ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Highly Efficient ◽  
Catalytic Sites ◽  
Catalytically Active ◽  
Doped Graphene ◽  
Waking Up

Numerous experiments have demonstrated that the metal atom is the active center of monoatomic catalysts for hydrogen evolution reaction (HER), while the active sites of nonmetal doped atoms are often neglected. By combining theoretical prediction and experimental verification, we designed a unique ternary Ru-N4-P coordination structure constructed by monodispersed Ru atoms supported on N,P dual-doped graphene for highly efficient hydrogen evolution in acid solution. The density functional theory calculations indicate that the charge polarization will lead to the most charge accumulation at P atoms, which results in a distinct nonmetallic P active sites with the moderate H∗ adsorption energy. Notably, these P atoms mainly supply highly efficient catalytic sites with ultrasmall absorption energy of 0.007 eV. Correspondingly, the Ru-N4-P demonstrated outstanding HER performance not only in an acidic condition but also in alkaline environment. Notably, the performance of Ru-NPC catalyst at high current is even superior to the commercial Pt/C catalysts, whether in acidic or alkaline medium. Our in situ synchrotron radiation infrared spectra demonstrate that a P-Hads intermediate is continually emerging on the Ru-NPC catalyst, actively proving the nonmetallic P catalytically active site in HER that is very different with previously reported metallic sites.

scholarly journals Glucose-6-Phosphate Dehydrogenase::6-Phosphogluconolactonase from the Parasite Giardia lamblia. A Molecular and Biochemical Perspective of a Fused Enzyme

2021 ◽  
Vol 9 (8) ◽  
pp. 1678
Author(s):  
Laura Morales-Luna ◽  
Abigail González-Valdez ◽  
Beatriz Hernández-Ochoa ◽  
Roberto Arreguin-Espinosa ◽  
Daniel Ortega-Cuellar ◽  
...  
Keyword(s):  
Giardia Lamblia ◽  
Drug Target ◽  
Active Sites ◽  
Reaction Medium ◽  
Structural Difference ◽  
Pentose Phosphate ◽  
Catalytically Active ◽  
The Individual ◽  
Glucose 6 Phosphate Dehydrogenase

Giardia lamblia is a single-celled eukaryotic parasite with a small genome and is considered an early divergent eukaryote. The pentose phosphate pathway (PPP) plays an essential role in the oxidative stress defense of the parasite and the production of ribose-5-phosphate. In this parasite, the glucose-6-phosphate dehydrogenase (G6PD) is fused with the 6-phosphogluconolactonase (6PGL) enzyme, generating the enzyme named G6PD::6PGL that catalyzes the first two steps of the PPP. Here, we report that the G6PD::6PGL is a bifunctional enzyme with two catalytically active sites. We performed the kinetic characterization of both domains in the fused G6PD::6PGL enzyme, as well as the individual cloned G6PD. The results suggest that the catalytic activity of G6PD and 6PGL domains in the G6PD::6PGL enzyme are more efficient than the individual proteins. Additionally, using enzymatic and mass spectrometry assays, we found that the final metabolites of the catalytic reaction of the G6PD::6PGL are 6-phosphoglucono-δ-lactone and 6-phosphogluconate. Finally, we propose the reaction mechanism in which the G6PD domain performs the catalysis, releasing 6-phosphoglucono-δ-lactone to the reaction medium. Then, this metabolite binds to the 6PGL domain catalyzing the hydrolysis reaction and generating 6-phosphogluconate. The structural difference between the G. lamblia fused enzyme G6PD::6PGL with the human G6PD indicate that the G6PD::6PGL is a potential drug target for the rational synthesis of novels anti-Giardia drugs.

scholarly journals Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK

2012 ◽  
Vol 367 (1602) ◽  
pp. 2656-2668 ◽  
Author(s):  
Jimin Zheng ◽  
Susan P. Yates ◽  
Zongchao Jia
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Isocitrate Dehydrogenase ◽  
Krebs Cycle ◽  
Evolutionary Relationship ◽  
Bifunctional Enzyme ◽  
Eukaryotic Protein Kinase ◽  
Glyoxylate Bypass ◽  
Regulatory Motifs

The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.

scholarly journals Characterization of the Interaction between the Nuclease and Reverse Transcriptase Activity of the Yeast Telomerase Complex

2000 ◽  
Vol 20 (18) ◽  
pp. 6806-6815 ◽  
Author(s):  
Hongwu Niu ◽  
Jinqiang Xia ◽  
Neal F. Lue
Keyword(s):  
Reverse Transcriptase ◽  
Active Site ◽  
Active Sites ◽  
Biochemical Properties ◽  
Reverse Transcriptase Activity ◽  
Transcriptase Activity ◽  
Yeast Telomerase ◽  
Enzyme Cleavage ◽  
Enzyme Cleavage Site

ABSTRACT Telomerase is a ribonucleoprotein that mediates extension of the dG-rich strand of telomeres in most eukaryotes. Like telomerase derived from ciliated protozoa, yeast telomerase is found to possess a tightly associated endonuclease activity that copurifies with the polymerization activity over different affinity-chromatographic steps. As is the case for ciliate telomerase, primers containing sequences that are not complementary to the RNA template can be efficiently cleaved by the yeast enzyme. More interestingly, we found that for the yeast enzyme, cleavage site selection is not stringent, since blocking cleavage at one site by the introduction of a nonhydrolyzable linkage can lead to the utilization of other sites. In addition, the reverse transcriptase activity of yeast telomerase can extend either the 5′- or 3′-end fragment following cleavage. Two general models that are consistent with the biochemical properties of the enzyme are presented: one model postulates two distinct active sites for the nuclease and reverse transcriptase, and the other invokes a multimeric enzyme with each protomer containing a single active site capable of mediating both cleavage and extension.

Precise identification and characterization of catalytically active sites on the surface of γ‐alumina

2021 ◽  
Author(s):  
Konstantin Khivantsev ◽  
Nicholas R. Jaegers ◽  
Ja-Hun Kwak ◽  
Janos Szanyi ◽  
Libor Kovarik
Keyword(s):  
Active Sites ◽  
Precise Identification ◽  
Catalytically Active ◽  
Identification And Characterization
Sign in / Sign up

Export Citation Format

Share Document