Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase
Abstract
5-Carboxyvanillate decarboxylase (LigW) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. This enzyme was shown to require Mn2+ for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s–1 and kcat/Km = 4.0 × 104 M–1 s–1) and Novosphingobium aromaticivorans (kcat = 27 s–1 and kcat/Km = 1.1 × 105 M–1 s–1) were determined. The three-dimensional structures of both enzymes were determined in the presence and absence of ligands bound in the active site. The structure of LigW from N. aromaticivorans, bound with the substrate analogue, 5-nitrovanillate (Kd = 5.0 nM), was determined to a resolution of 1.07 Å. The structure of this complex shows a remarkable enzyme-induced distortion of the nitro-substituent out of the plane of the phenyl ring by approximately 23°. A chemical reaction mechanism for the decarboxylation of 5-carboxyvanillate by LigW was proposed on the basis of the high resolution X-ray structures determined in the presence ligands bound in the active site, mutation of active site residues, and the magnitude of the product isotope effect determined in a mixture of H2O and D2O. In the proposed reactionmore »
- Authors:
-
- Department of Chemistry, Texas A&,M University, College Station, Texas 77843, United States
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
- OSTI Identifier:
- 1234469
- Alternate Identifier(s):
- OSTI ID: 1354563
- Report Number(s):
- BNL-113080-2016-JA
Journal ID: ISSN 0002-7863
- Grant/Contract Number:
- SC00112704; GM 71790
- Resource Type:
- Published Article
- Journal Name:
- Journal of the American Chemical Society
- Additional Journal Information:
- Journal Name: Journal of the American Chemical Society Journal Volume: 138 Journal Issue: 3; Journal ID: ISSN 0002-7863
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Chemical structure; Hydroxyls; Peptides and proteins; Reaction mechanisms; Organic reactions
Citation Formats
Vladimirova, Anna, Patskovsky, Yury, Fedorov, Alexander A., Bonanno, Jeffrey B., Fedorov, Elena V., Toro, Rafael, Hillerich, Brandan, Seidel, Ronald D., Richards, Nigel G. J., Almo, Steven C., and Raushel, Frank M. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase. United States: N. p., 2016.
Web. doi:10.1021/jacs.5b08251.
Vladimirova, Anna, Patskovsky, Yury, Fedorov, Alexander A., Bonanno, Jeffrey B., Fedorov, Elena V., Toro, Rafael, Hillerich, Brandan, Seidel, Ronald D., Richards, Nigel G. J., Almo, Steven C., & Raushel, Frank M. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase. United States. https://doi.org/10.1021/jacs.5b08251
Vladimirova, Anna, Patskovsky, Yury, Fedorov, Alexander A., Bonanno, Jeffrey B., Fedorov, Elena V., Toro, Rafael, Hillerich, Brandan, Seidel, Ronald D., Richards, Nigel G. J., Almo, Steven C., and Raushel, Frank M. Tue .
"Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase". United States. https://doi.org/10.1021/jacs.5b08251.
@article{osti_1234469,
title = {Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase},
author = {Vladimirova, Anna and Patskovsky, Yury and Fedorov, Alexander A. and Bonanno, Jeffrey B. and Fedorov, Elena V. and Toro, Rafael and Hillerich, Brandan and Seidel, Ronald D. and Richards, Nigel G. J. and Almo, Steven C. and Raushel, Frank M.},
abstractNote = {5-Carboxyvanillate decarboxylase (LigW) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. This enzyme was shown to require Mn2+ for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s–1 and kcat/Km = 4.0 × 104 M–1 s–1) and Novosphingobium aromaticivorans (kcat = 27 s–1 and kcat/Km = 1.1 × 105 M–1 s–1) were determined. The three-dimensional structures of both enzymes were determined in the presence and absence of ligands bound in the active site. The structure of LigW from N. aromaticivorans, bound with the substrate analogue, 5-nitrovanillate (Kd = 5.0 nM), was determined to a resolution of 1.07 Å. The structure of this complex shows a remarkable enzyme-induced distortion of the nitro-substituent out of the plane of the phenyl ring by approximately 23°. A chemical reaction mechanism for the decarboxylation of 5-carboxyvanillate by LigW was proposed on the basis of the high resolution X-ray structures determined in the presence ligands bound in the active site, mutation of active site residues, and the magnitude of the product isotope effect determined in a mixture of H2O and D2O. In the proposed reaction mechanism the enzyme facilitates the transfer of a proton to C5 of the substrate prior to the decarboxylation step.},
doi = {10.1021/jacs.5b08251},
journal = {Journal of the American Chemical Society},
number = 3,
volume = 138,
place = {United States},
year = {Tue Jan 12 00:00:00 EST 2016},
month = {Tue Jan 12 00:00:00 EST 2016}
}
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