Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase

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.

doi:10.1021/jacs.5b08251

Title: Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase

Journal Article · Tue Jan 12 00:00:00 EST 2016 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/jacs.5b08251· OSTI ID:1234469

Vladimirova, Anna ^[1]; Patskovsky, Yury ^[2]; Fedorov, Alexander A. ^[2]; Bonanno, Jeffrey B. ^[2]; Fedorov, Elena V. ^[2]; Toro, Rafael ^[2]; Hillerich, Brandan ^[2]; Seidel, Ronald D. ^[2]; Richards, Nigel G. J. ^[3]; Almo, Steven C. ^[2]; Raushel, Frank M. ^[1]

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

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 (k_cat = 2.2 s^–1 and k_cat/K_m = 4.0 × 10⁴ M^–1 s^–1) and Novosphingobium aromaticivorans (k_cat = 27 s^–1 and k_cat/K_m = 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 (K_d = 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.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)

Grant/Contract Number:: SC00112704; GM 71790

OSTI ID:: 1234469

Alternate ID(s):: OSTI ID: 1354563

Report Number(s):: BNL-113080-2016-JA

Journal Information:: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Vol. 138 Journal Issue: 3; ISSN 0002-7863

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 33 works

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