Insights into the catalytic mechanism of synthetic glutathione peroxidase mimetics

2015 ◽  
Vol 13 (41) ◽  
pp. 10262-10272 ◽  
Author(s):  
Debasish Bhowmick ◽  
Govindasamy Mugesh
Keyword(s):  
Glutathione Peroxidase ◽  
Catalytic Mechanism ◽  
Catalytic Mechanisms

This review focuses on the variation of the catalytic mechanisms of synthetic glutathione peroxidase (GPx) mimics depending on their structures and reactivities towards thiols and peroxides. Compounds of different categories follow a characteristic mechanism for the reduction of peroxides.

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 A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

scholarly journals Catalytic mechanism of the glutathione peroxidase-type tryparedoxin peroxidase of Trypanosoma brucei

2007 ◽  
Vol 405 (3) ◽  
pp. 445-454 ◽  
Author(s):  
Tanja Schlecker ◽  
Marcelo A. Comini ◽  
Johannes Melchers ◽  
Thomas Ruppert ◽  
R. Luise Krauth-Siegel
Keyword(s):  
Glutathione Peroxidase ◽  
Trypanosoma Brucei ◽  
Catalytic Mechanism ◽  
Disulfide Bridge ◽  
Catalytic Triad ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Glutathione Peroxidases ◽  
Thiolate Anion ◽  
In The Wild

Trypanosoma brucei, the causative agent of African sleeping sickness, encodes three nearly identical genes for cysteine-homologues of the selenocysteine-containing glutathione peroxidases. The enzymes, which are essential for the parasites, lack glutathione peroxidase activity but catalyse the trypanothione/Tpx (tryparedoxin)-dependent reduction of hydroperoxides. Cys47, Gln82 and Trp137 correspond to the selenocysteine, glutamine and tryptophan catalytic triad of the mammalian selenoenzymes. Site-directed mutagenesis revealed that Cys47 and Gln82 are essential. A glycine mutant of Trp137 had 13% of wild-type activity, which suggests that the aromatic residue may play a structural role but is not directly involved in catalysis. Cys95, which is conserved in related yeast and plant proteins but not in the mammalian selenoenzymes, proved to be essential as well. In contrast, replacement of the highly conserved Cys76 by a serine residue resulted in a fully active enzyme species and its role remains unknown. Thr50, proposed to stabilize the thiolate anion at Cys47, is also not essential for catalysis. Treatment of the C76S/C95S but not of the C47S/C76S double mutant with H2O2 induced formation of a sulfinic acid and covalent homodimers in accordance with Cys47 being the peroxidative active site thiol. In the wild-type peroxidase, these oxidations are prevented by formation of an intramolecular disulfide bridge between Cys47 and Cys95. As shown by MS, regeneration of the reduced enzyme by Tpx involves a transient mixed disulfide between Cys95 of the peroxidase and Cys40 of Tpx. The catalytic mechanism of the Tpx peroxidase resembles that of atypical 2-Cys-peroxiredoxins but is distinct from that of the selenoenzymes.

Structure of Hydrogenase in Biohydrogen Production Anaerobic Bacteria

2011 ◽  
pp. 251-258 ◽  
Author(s):  
Ming Du ◽  
Lu Zhang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Anaerobic Bacteria ◽  
Research Direction ◽  
Biohydrogen Production ◽  
Future Research ◽  
Hydrogen Energy ◽  
Industrialization Process ◽  
Catalytic Mechanisms

Hydrogenase plays an important role in the process of biohydrogen production. Hydrogenases have very unique active sites and are classified into three groups according to the metal composition of the active sites: the [Ni-Fe] hydrogenase, [Fe-Fe] hydrogenase, and [Fe-only] hydrogenase. In this paper, the crystal structures and active sites of three kinds of hydrogenases are examined and compared. These enzymes have an unusual structural feature in common. Their similar active site indicates that the catalytic mechanism of hydrogen activation is probably similar. The understanding of the catalytic mechanisms for the three kinds of hydrogenases may help achieve the industrialization process of hydrogen energy production. Moreover, the future research direction about the hydrogenases from auto-aggregative bacteria and the chemical mimic of hydrogenases structure is discussed.

X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form

1998 ◽  
Vol 54 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Andrea Carfi ◽  
Emile Duée ◽  
Raquel Paul-Soto ◽  
Moreno Galleni ◽  
Jean-Marie Frère ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Bacteroides Fragilis ◽  
Crystal Form ◽  
Water Molecules ◽  
Orthorhombic Crystal ◽  
X Ray ◽  
Class B ◽  
Catalytic Mechanisms ◽  
Zn Ions

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.

scholarly journals Alternative catalytic mechanisms driven by structural plasticity is an emerging theme in HAS-GTPases, Era and FeoB

2020 ◽  
Author(s):  
Sahil Batra ◽  
Ashok Kumar ◽  
Balaji Prakash
Keyword(s):  
Catalytic Mechanism ◽  
Structural Plasticity ◽  
Nucleophilic Attack ◽  
Hydrophobic Residue ◽  
Gtp Hydrolysis ◽  
Primary Mechanism ◽  
Transition State Analogue ◽  
Physiological Relevance ◽  
Underlying Basis ◽  
Catalytic Mechanisms

AbstractGTP hydrolysis is the underlying basis for functioning of ‘biological switches’ or GTPases. Extensively studied GTPases, Ras and EF-Tu, use a conserved Gln/His that facilitates the activation of attacking water for nucleophilic attack. However, this is insufficient to explain catalysis in Hydrophobic Amino acid Substituted (HAS)-GTPases that naturally possess a hydrophobic residue in lieu of Gln/His. We had previously reported a bridging water-chain mediated catalytic mechanism for HAS-GTPase FeoB; which utilizes two distantly-located but conserved glutamates. Curiously, mutating these does not abolish GTP hydrolysis. Similarly, in this study we report our observations on another HAS-GTPase Era, wherein the mutants of catalytically important residues continue to hydrolyze GTP. We attempt to rationalize these inquisitive observations on GTP hydrolysis by FeoB and Era mutants. We propose a general theory that appears common to at least three classes of GTPases, where ‘alternative mechanisms’ emerge when the primary mechanism is disrupted. Based on the analysis of crystal structures of FeoB and Era mutants, bound to the transition state analogue GDP.AlFx, this work suggests that in the absence of catalytically important residues, the active site waters in both FeoB and Era undergo re-arrangements, which in turn helps in sustaining GTP hydrolysis. Similar employment of alternative mechanisms was also suggested for the catalytic mutants of hGBP1. Importantly, such alternatives underscore the robustness of GTP hydrolysis mechanisms in these systems, and raise important questions regarding the need for persistent GTP hydrolysis and the physiological relevance of structural plasticity seen here.

The synthesis of some mechanistic probes for sialic acid processing enzymes and the labeling of a sialidase from Trypanosoma rangeli

2004 ◽  
Vol 82 (11) ◽  
pp. 1581-1588 ◽  
Author(s):  
Andrew G Watts ◽  
Stephen G Withers
Keyword(s):  
Sialic Acid ◽  
Catalytic Mechanism ◽  
Competitive Inhibitor ◽  
Enzymatic Process ◽  
Trypanosoma Rangeli ◽  
Available N ◽  
Processing Enzymes ◽  
Acid Processing ◽  
Catalytic Mechanisms ◽  
Enzyme Intermediate

Sialyl hydrolases, trans-sialidases, and sialyl transferases are biologically important enzymes that are responsible for the incorporation and removal of sialic acid residues, which decorate many cell surface glycocongugates. Two fluorinated sialic acid derivatives have been synthesized as mechanism-based inactivators, to probe the catalytic mechanisms through which sialidases and trans-sialidases operate. Both compounds are known to be covalent inactivators of a trans-sialidase from Trypanosoma cruzi. Here, 3-fluorosialosyl fluoride has been found to covalently label the catalytic nucleophile of a sialidase from T. rangeli, and the residue involved is shown to be Tyr346 within the sequence DENSGYSSVL. This is the first demonstration that sialidases operate through a covalent glycosyl-enzyme intermediate, strongly suggesting a common catalytic mechanism amongst all members of the sialidase superfamily. CMP-3-fluoro sialic acid is a competitive inhibitor of sialyl transferases and was synthesized via a two-step enzymatic process from commercially available N-acetyl mannosamine, 3-fluoropyruvic acid, and cytidine triphosphate in around 84% yield.Key words: sialidase, mechanism, labeling, nucleophile, inhibitor.

Metal and metal-oxide nanozymes: bioenzymatic characteristics, catalytic mechanism, and eco-environmental applications

Nanoscale ◽  
2019 ◽  
Vol 11 (34) ◽  
pp. 15783-15793 ◽  
Author(s):  
Wenjun Chen ◽  
Shunyao Li ◽  
Jun Wang ◽  
Kai Sun ◽  
Youbin Si
Keyword(s):  
Metal Oxide ◽  
Catalytic Mechanism ◽  
Environmental Applications ◽  
Enzymatic Characteristics ◽  
Catalytic Mechanisms

This review highlights the available studies on the enzymatic characteristics and catalytic mechanisms of natural enzymes and artificial metal and metal-oxide nanozymes in the removal and transformation of phenolic contaminants.

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