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Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs

Chen, Chao, Shrestha, Ruben, Jia, Kaimin, Gao, Philip F., Geisbrecht, Brian V., Bossmann, Stefan H., Shi, Jishu, Li, Ping·2015·Journal of Biological Chemistry
DOI 10.1074/jbc.m115.658807
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FIGURE 1 Comparison of sequences and structures. A, sequence alignment of four types of DyPs. Putative catalytic residues surrounding the heme center are highlighted. The fingerprint motif of DyPs is boxed . B, predicted structure and active site of Tc DyP using COACH based on a DyP-type peroxidase from Stretomyces coelicolor (Protein Data Bank code 4GRC). The sequence identity between the two proteins and C-score of the homology model are 42% and 0.98, respectively. C , structure and active site of HRP (Protein Data BAnk code 1ATJ).
FIGURE 1 Comparison of sequences and structures. A, sequence alignment of four types of DyPs. Putative catalytic residues surrounding the heme center are highlighted. The fingerprint motif of DyPs is boxed . B, predicted structure and active site of Tc DyP using COACH based on a DyP-type peroxidase from Stretomyces coelicolor (Protein Data Bank code 4GRC). The sequence identity between the two proteins and C-score of the homology model are 42% and 0.98, respectively. C , structure and active site of HRP (Protein Data BAnk code 1ATJ).CC-BY · From the PDF
FIGURE 2 Biochemical characterization of Tc DyP. A , SDS-PAGE of wt - and mutant Tc DyP. B , UV-visible spectra of wt-Tc DyPin apo ( dotted line ) and holo ( solid line ) forms. C , pyridine hemochrome assay of Tc DyPcalculated by the absorbance difference between the reduced ( solid line ) and oxidized ( dotted line ) spectra using 𝚫 𝛜 = 20.7 mM -1 cm -1 . D, rate pH profiles of wt -Tc DyP with ABTS ( solid line ), HQ ( dash line ), and guaiacol ( dotted line ). E, profiles of optimal assay temperature ( solid line ) and enzyme stability ( dotted line ).
FIGURE 2 Biochemical characterization of Tc DyP. A , SDS-PAGE of wt - and mutant Tc DyP. B , UV-visible spectra of wt-Tc DyPin apo ( dotted line ) and holo ( solid line ) forms. C , pyridine hemochrome assay of Tc DyPcalculated by the absorbance difference between the reduced ( solid line ) and oxidized ( dotted line ) spectra using 𝚫 𝛜 = 20.7 mM -1 cm -1 . D, rate pH profiles of wt -Tc DyP with ABTS ( solid line ), HQ ( dash line ), and guaiacol ( dotted line ). E, profiles of optimal assay temperature ( solid line ) and enzyme stability ( dotted line ).CC-BY · From the PDF
FIGURE 3 Profiles of enzyme activities. A, the wt -Tc DyP with various substrates. B , activities of wt and mutant enzymes with ABTS ( solid bar ), HQ ( line patterned bar ), and guaiacol ( cross-patterned bar ).
FIGURE 3 Profiles of enzyme activities. A, the wt -Tc DyP with various substrates. B , activities of wt and mutant enzymes with ABTS ( solid bar ), HQ ( line patterned bar ), and guaiacol ( cross-patterned bar ).CC-BY · From the PDF
Image 4
CC-BY · From the PDF
Image 5
CC-BY · From the PDF
FIGURE6 Reactionsof wt -Tc DyPwithH2O2. A , spectral transition of 5 𝛍 Menzymeand5 𝛍 MH2O2 atpH7.8( left ) and 3.0 ( right ) recorded in 2.0 s. The blue , green , and red lines represent Tc DyP-0, Tc DyP-I, and decay product, respectively. Arrows indicate changes of absorbance over time. B, typical time trace at 406 nm ( left ) and dependence of k obs (406 nm) versus [H2 O2] ( right ) for Tc DyP-I formation at pH 7.8. C, typical time trace at 416 nm ( left ) and dependence of k obs (416 nm) versus [H2 O2] ( right ) for decay of Tc DyP-I at pH 7.8. D, same as B except that the pH was 3.0.
FIGURE6 Reactionsof wt -Tc DyPwithH2O2. A , spectral transition of 5 𝛍 Menzymeand5 𝛍 MH2O2 atpH7.8( left ) and 3.0 ( right ) recorded in 2.0 s. The blue , green , and red lines represent Tc DyP-0, Tc DyP-I, and decay product, respectively. Arrows indicate changes of absorbance over time. B, typical time trace at 406 nm ( left ) and dependence of k obs (406 nm) versus [H2 O2] ( right ) for Tc DyP-I formation at pH 7.8. C, typical time trace at 416 nm ( left ) and dependence of k obs (416 nm) versus [H2 O2] ( right ) for decay of Tc DyP-I at pH 7.8. D, same as B except that the pH was 3.0.CC-BY · From the PDF
FIGURE 7 Reactions of Tc DyP-I with HQ in a sequential mixing mode. A, spectral transition of 3 mM HQ and Tc DyP-I at pH 7.8 ( top ) and 3.0 ( bottom ) recorded in 1.0 s. The green and red lines represent Tc DyP-I and Tc DyP-II, respectively. Arrows indicate changes of absorbance over time. B, typical time trace at 416 nm ( left ) and dependence of k obs (416 nm) versus [HQ] ( right ) for Tc DyP-II formation at pH 7.8.
FIGURE 7 Reactions of Tc DyP-I with HQ in a sequential mixing mode. A, spectral transition of 3 mM HQ and Tc DyP-I at pH 7.8 ( top ) and 3.0 ( bottom ) recorded in 1.0 s. The green and red lines represent Tc DyP-I and Tc DyP-II, respectively. Arrows indicate changes of absorbance over time. B, typical time trace at 416 nm ( left ) and dependence of k obs (416 nm) versus [HQ] ( right ) for Tc DyP-II formation at pH 7.8.CC-BY · From the PDF
FIGURE 8 Reductions of Tc DyP-II with HQ in a sequential mixing mode. A, spectral transition of 5 mM HQ and Tc DyP-II at pH 3.0 recorded in 1.0 s. The blue and red lines represent Tc DyP-0 and Tc DyP-II, respectively. Arrows indicate changes of absorbance over time. B , typical time trace at 406 nm ( left panel ) and dependence of k obs (406 nm) versus [HQ] ( right panel ) for Tc DyP-II reduction.
FIGURE 8 Reductions of Tc DyP-II with HQ in a sequential mixing mode. A, spectral transition of 5 mM HQ and Tc DyP-II at pH 3.0 recorded in 1.0 s. The blue and red lines represent Tc DyP-0 and Tc DyP-II, respectively. Arrows indicate changes of absorbance over time. B , typical time trace at 406 nm ( left panel ) and dependence of k obs (406 nm) versus [HQ] ( right panel ) for Tc DyP-II reduction.CC-BY · From the PDF
Image 9
CC-BY · From the PDF
Image 10
CC-BY · From the PDF
FIGURE 10 Formation and reduction of Tc DyP-II with H312A. The reactions were performed in a sequential mixing mode. Arrows indicate changes of absorbance over time. A, spectral transition of 5 mM HQ and 5 𝛍 M Tc DyP-I at pH7.8 recorded in 1.0 s (formation of Tc DyP-II). The green and red lines represent Tc DyP-I and Tc DyP-II, respectively. B, spectral transition of 5 mM HQ and 5 𝛍 M Tc DyP-II at pH 3.0 recorded in 10 s (reduction of Tc DyP-II). The blue , green , and red lines represent Tc DyP-II, an intermediate state at 30 ms, and formed new species, respectively.
FIGURE 10 Formation and reduction of Tc DyP-II with H312A. The reactions were performed in a sequential mixing mode. Arrows indicate changes of absorbance over time. A, spectral transition of 5 mM HQ and 5 𝛍 M Tc DyP-I at pH7.8 recorded in 1.0 s (formation of Tc DyP-II). The green and red lines represent Tc DyP-I and Tc DyP-II, respectively. B, spectral transition of 5 mM HQ and 5 𝛍 M Tc DyP-II at pH 3.0 recorded in 10 s (reduction of Tc DyP-II). The blue , green , and red lines represent Tc DyP-II, an intermediate state at 30 ms, and formed new species, respectively.CC-BY · From the PDF
Image 12
CC-BY · From the PDF
FIGURE 12 SEC profile of Tc DyP. The standard curve is shown as the inset .
FIGURE 12 SEC profile of Tc DyP. The standard curve is shown as the inset .CC-BY · From the PDF
FIGURE 13 Catalytic cycle of wt -Tc DyP. Second-order rate constants are shown for each step.
FIGURE 13 Catalytic cycle of wt -Tc DyP. Second-order rate constants are shown for each step.CC-BY · From the PDF

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Authors
Chen, C., Shrestha, R., Jia, K., Gao, P. F., Geisbrecht, B. V., Bossmann, S. H., Shi, J., & Li, P.
Venue
Journal of Biological Chemistry
Publisher
Elsevier BV
Published
2015-09
Volume
290
Issue
38
Pages
23447-23463
ISSN
0021-9258
DOI
10.1074/jbc.m115.658807
Cited by
124
References
1
Language
en
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