Cleavage of models for RNA mediated by a diZn(II) complex of bis[1,4-N1,N1′(1,5,9-triazacyclododecanyl)]butane in methanol and ethanol

2009 ◽  
Vol 87 (5) ◽  
pp. 640-649 ◽  
Author(s):  
C. Tony Liu ◽  
Stephanie A. Melnychuk ◽  
Chaomin Liu ◽  
Alexei A. Neverov ◽  
R. Stan Brown
Keyword(s):  
Transition State ◽  
Linear Dependence ◽  
Catalyst Concentration ◽  
Active Form ◽  
Catalytic Efficiency ◽  
Saturation Binding ◽  
Controlled Conditions ◽  
Versus Complex ◽  
Leaving Groups ◽  
Ph Controlled

The cleavage of seven RNA model 2-hydroxypropyl aryl phosphates (1) catalyzed by a dinuclear Zn(II) complex of bis[1,4-N1,N1′(1,5,9-triazacyclododecanyl)]butane (4) was studied in methanol and ethanol at 25 °C under pH controlled conditions. The results are compared with what was reported earlier for the dinuclear Zn(II) complex of the lower homologue bis[1,3-N1,N1′(1,5,9-triazacyclododecanyl)]propane (3). In methanol, the higher homologue exhibits saturation binding with substrates having poor aryloxy leaving groups. With good leaving groups there is an observed linear dependence of kobs versus complex concentration without saturation binding over the catalyst concentration range investigated. In ethanol, strong saturation binding between the active form of the catalyst ((RO–):Zn(II)2:4) and all substrates is observed, the results observed in both solvents being similar to what was reported for the lower (RO–):Zn(II)2:3 homologue. Energetics calculations are presented for the (RO–):Zn(II)2:4-catalyzed cleavage of each substrate in both solvents to assess the catalytic efficiency via the ΔΔG‡ for catalyst binding a transition state comprising [RO–:1]‡ or its kinetic equivalent.

α-Retaining glucosyl transfer catalysed by trehalose phosphorylase from Schizophyllum commune: mechanistic evidence obtained from steady-state kinetic studies with substrate analogues and inhibitors

2001 ◽  
Vol 360 (3) ◽  
pp. 727-736 ◽  
Author(s):  
Bernd NIDETZKY ◽  
Christian EIS
Keyword(s):  
Steady State ◽  
Transition State ◽  
Schizophyllum Commune ◽  
Catalytic Efficiency ◽  
Kinetic Studies ◽  
Competitive Inhibitor ◽  
Chemical Mechanism ◽  
Steady State Kinetic ◽  
State Kinetic ◽  
Trehalose Phosphorylase

Fungal trehalose phosphorylase is classified as a family 4 glucosyltransferase that catalyses the reversible phosphorolysis of α,α-trehalose with net retention of anomeric configuration. Glucosyl transfer to and from phosphate takes place by the partly rate-limiting interconversion of ternary enzyme–substrate complexes formed from binary enzyme–phosphate and enzyme–α-d-glucopyranosyl phosphate adducts respectively. To advance a model of the chemical mechanism of trehalose phosphorylase, we performed a steady-state kinetic study with the purified enzyme from the basidiomycete fungus Schizophyllum commune by using alternative substrates, inhibitors and combinations thereof in pairs as specific probes of substrate-binding recognition and transition-state structure. Orthovanadate is a competitive inhibitor against phosphate and α-d-glucopyranosyl phosphate, and binds 3×104-fold tighter (Ki≈ 1μM) than phosphate. Structural alterations of d-glucose at C-2 and O-5 are tolerated by the enzyme at subsite +1. They lead to parallel effects of approximately the same magnitude (slope = 1.14; r2 = 0.98) on the reciprocal catalytic efficiency for reverse glucosyl transfer [log (Km/kcat)] and the apparent affinity of orthovanadate determined in the presence of the respective glucosyl acceptor (log Ki). An adduct of orthovanadate and the nucleophile/leaving group bound at subsite +1 is therefore the true inhibitor and displays partial transition state analogy. Isofagomine binds to subsite −1 in the enzyme–phosphate complex with a dissociation constant of 56μM and inhibits trehalose phosphorylase at least 20-fold better than 1-deoxynojirimycin. The specificity of the reversible azasugars inhibitors would be explained if a positive charge developed on C-1 rather than O-5 in the proposed glucosyl cation-like transition state of the reaction. The results are discussed in the context of α-retaining glucosyltransferase mechanisms that occur with and without a β-glucosyl enzyme intermediate.

scholarly journals The human fibrinolytic system is a target for the staphylococcal metalloprotease aureolysin

2008 ◽  
Vol 410 (1) ◽  
pp. 157-165 ◽  
Author(s):  
Nathalie Beaufort ◽  
Piotr Wojciechowski ◽  
Christian P. Sommerhoff ◽  
Grzegorz Szmyd ◽  
Grzegorz Dubin ◽  
...  
Keyword(s):  
Plasminogen Activator ◽  
Active Form ◽  
Catalytic Efficiency ◽  
Plasminogen Activator Inhibitor ◽  
Opportunistic Pathogen ◽  
Fibrinolytic System ◽  
Growth Media ◽  
Single Chain ◽  
Plasminogen Activator Inhibitor 1 ◽  
Proteolytic Activation

The major opportunistic pathogen Staphylococcus aureus utilizes the human fibrinolytic system for invasion and spread via plasmin(ogen) binding and non-proteolytic activation. Because S. aureus secretes several proteases recently proposed as virulence factors, we explored whether these enzymes could add to the activation of the host's fibrinolytic system. Exposure of human pro-urokinase [pro-uPA (where uPA is urokinase-type plasminogen activator)] to conditioned growth media from staphylococcal reference strains results in an EDTA-sensitive conversion of the single-chain zymogen into its two-chain active form, an activity not observed in an aureolysin-deficient strain. Using purified aureolysin, we verified the capacity of this thermolysin-like metalloprotease to activate pro-uPA, with a 2.6×103 M−1·s−1 catalytic efficiency. Moreover, activation also occurs in the presence of human plasma, as well as in conditioned growth media from clinical isolates. Finally, we establish that aureolysin (i) converts plasminogen into angiostatin and mini-plasminogen, the latter retaining its capacity to be activated by uPA and to hydrolyse fibrin, (ii) degrades the plasminogen activator inhibitor-1, and (iii) abrogates the inhibitory activity of α2-antiplasmin. Altogether, we propose that, in parallel with the staphylokinase-dependent activation of plasminogen, aureolysin may contribute significantly to the activation of the fibrinolytic system by S. aureus, and thus may promote bacterial spread and invasion.

scholarly journals Phosphoenolpyruvate Synthetase from the Hyperthermophilic Archaeon Pyrococcus furiosus

2001 ◽  
Vol 183 (2) ◽  
pp. 709-715 ◽  
Author(s):  
Andrea M. Hutchins ◽  
James F. Holden ◽  
Michael W. W. Adams
Keyword(s):  
Molecular Mass ◽  
Functional Role ◽  
Pyrococcus Furiosus ◽  
Active Form ◽  
Catalytic Efficiency ◽  
Maximal Activity ◽  
Kinetic Properties ◽  
Additional Function ◽  
Hyperthermophilic Archaeon ◽  
A Subunit

ABSTRACT Phosphoenolpyruvate synthetase (PpsA) was purified from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme catalyzes the conversion of pyruvate and ATP to phosphoenolpyruvate (PEP), AMP, and phosphate and is thought to function in gluconeogenesis. PpsA has a subunit molecular mass of 92 kDa and contains one calcium and one phosphorus atom per subunit. The active form has a molecular mass of 690 ± 20 kDa and is assumed to be octomeric, while approximately 30% of the protein is purified as a large (∼1.6 MDa) complex that is not active. The apparentKm values and catalytic efficiencies for the substrates pyruvate and ATP (at 80°C, pH 8.4) were 0.11 mM and 1.43 × 104 mM−1 · s−1 and 0.39 mM and 3.40 × 103mM−1 · s−1, respectively. Maximal activity was measured at pH 9.0 (at 80°C) and at 90°C (at pH 8.4). The enzyme also catalyzed the reverse reaction, but the catalytic efficiency with PEP was very low [k cat/Km = 32 (mM · s)−1]. In contrast to several other nucleotide-dependent enzymes from P. furiosus, PpsA has an absolute specificity for ATP as the phosphate-donating substrate. This is the first PpsA from a nonmethanogenic archaeon to be biochemically characterized. Its kinetic properties are consistent with a role in gluconeogenesis, although its relatively high cellular concentration (∼5% of the cytoplasmic protein) suggests an additional function possibly related to energy spilling. It is not known whether interconversion between the smaller, active and larger, inactive forms of the enzyme has any functional role.

Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity

2013 ◽  
Vol 451 (2) ◽  
pp. 217-226 ◽  
Author(s):  
Emily Golden ◽  
Rachel Paterson ◽  
Wan Jun Tie ◽  
Anandhi Anandan ◽  
Gavin Flematti ◽  
...  
Keyword(s):  
Transition State ◽  
Active Site ◽  
Catalytic Efficiency ◽  
Cephalosporin C ◽  
Class Iii ◽  
Wild Type ◽  
Serine Residue ◽  
Active Site Cavity ◽  
Β Chain ◽  
Enzyme Variant

The crystal structure of the wild-type form of glutaryl-7-ACA (7-aminocephalosporanic acid) acylase from Pseudomonas N176 and a double mutant of the protein (H57βS/H70βS) that displays enhanced catalytic efficiency on cephalosporin C over glutaryl-7-aminocephalosporanic acid has been determined. The structures show a heterodimer made up of an α-chain (229 residues) and a β-chain (543 residues) with a deep cavity, which constitutes the active site. Comparison of the wild-type and mutant structures provides insights into the molecular reasons for the observed enhanced specificity on cephalosporin C over glutaryl-7-aminocephalosporanic acid and offers the basis to evolve a further improved enzyme variant. The nucleophilic catalytic serine residue, Ser1β, is situated at the base of the active site cavity. The electron density reveals a ligand covalently bound to the catalytic serine residue, such that a tetrahedral adduct is formed. This is proposed to mimic the transition state of the enzyme for both the maturation step and the catalysis of the substrates. A view of the transition state configuration of the enzyme provides important insights into the mechanism of substrate binding and catalysis.

DNA Polymerase β Fidelity:  Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State†

Biochemistry ◽  
2008 ◽  
Vol 47 (3) ◽  
pp. 870-879 ◽  
Author(s):  
Christopher A. Sucato ◽  
Thomas G. Upton ◽  
Boris A. Kashemirov ◽  
Jorge Osuna ◽  
Keriann Oertell ◽  
...  
Keyword(s):  
Steady State ◽  
Transition State ◽  
Kinetic Analysis ◽  
Dna Polymerase ◽  
Dna Polymerase Β ◽  
Steady State Kinetic ◽  
Leaving Groups ◽  
State Kinetic
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