Complexes Between m-chloroperoxybenzoic Acid and Horseradish Peroxidase Compounds I and II: Implications for the Kinetics of Enzyme Inactivation

Hiner, Alexander N.P.; Ruiz, Josefa Hernández; Arnao, Marino B.; López, José García; Cánovas, Fernando; Acosta, Manuel

doi:10.1080/1475636021000016990

Cited by 4 publications

(1 citation statement)

References 7 publications

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“…1(A). The time progress curves of [E] and [ES] were obtained by numerical integration of the set of differential equations (A.1)-(A.6) in Appendix A using for the rate constants and initial concentration of the free enzyme, [E] 0 , the same values given in Table 1 the experimental time progress curve of the residual enzyme activity (Hiner et al, , 2002Rodriguez-Lopez et al, 2001;Gilabert et al, 2004aGilabert et al, , 2004b, the product accumulation (Garrido del Solo et al, 1993), or the substrate release (Varon et al, 1994;Duggleby, 1986).…”

Section: Application To An Experimental Design and A Kinetic Data Anamentioning

confidence: 99%

Mean Lifetime and First-Passage Time of the Enzyme Species Involved in an Enzyme Reaction. Application to Unstable Enzyme Systems

et al. 2008

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Taking as starting point the complete analysis of mean residence times in linear compartmental systems performed by Garcia-Meseguer et al. (Bull. Math. Biol. 65:279-308, 2003) as well as the fact that enzyme systems, in which the interconversions between the different enzyme species involved are of first or pseudofirst order, act as linear compartmental systems, we hereby carry out a complete analysis of the mean lifetime that the enzyme molecules spend as part of the enzyme species, forms, or groups involved in an enzyme reaction mechanism. The formulas to evaluate these times are given as a function of the individual rate constants and the initial concentrations of the involved species at the onset of the reaction. We apply the results to unstable enzyme systems and support the results by using a concrete example of such systems. The practicality of obtaining the mean times and their possible application in a kinetic data analysis is discussed.

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Section: Application To An Experimental Design and A Kinetic Data Anamentioning

confidence: 99%

Mean Lifetime and First-Passage Time of the Enzyme Species Involved in an Enzyme Reaction. Application to Unstable Enzyme Systems

et al. 2008

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Crystal structures of two novel dye‐decolorizing peroxidases reveal a β‐barrel fold with a conserved heme‐binding motif

et al. 2007

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BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

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Identification and structural characterization of heme binding in a novel dye‐decolorizing peroxidase, TyrA

et al. 2007

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TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases.

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Complexes Between m-chloroperoxybenzoic Acid and Horseradish Peroxidase Compounds I and II: Implications for the Kinetics of Enzyme Inactivation

Cited by 4 publications

References 7 publications

Mean Lifetime and First-Passage Time of the Enzyme Species Involved in an Enzyme Reaction. Application to Unstable Enzyme Systems

Mean Lifetime and First-Passage Time of the Enzyme Species Involved in an Enzyme Reaction. Application to Unstable Enzyme Systems

Crystal structures of two novel dye‐decolorizing peroxidases reveal a β‐barrel fold with a conserved heme‐binding motif

Identification and structural characterization of heme binding in a novel dye‐decolorizing peroxidase, TyrA

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