Mechanism and Structure of γ-Resorcylate Decarboxylase

Xiang Sheng, Yury Patskovsky, Anna Vladimirova, Jeffrey B. Bonanno, Steven C. Almo, Fahmi Himo, Frank M. Raushel

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.

Original languageEnglish (US)
Pages (from-to)3167-3175
Number of pages9
JournalBiochemistry
Volume57
Issue number22
DOIs
StatePublished - Jun 5 2018

Fingerprint

Carboxy-Lyases
Decarboxylation
Catalytic Domain
Rhizobium
Enzymes
Benzoic Acid
Substrates
Manganese
Density functional theory
Anions
Protons
Crystal structure
Ions
Oxygen
Derivatives
Kinetics

ASJC Scopus subject areas

  • Biochemistry

Cite this

Sheng, X., Patskovsky, Y., Vladimirova, A., Bonanno, J. B., Almo, S. C., Himo, F., & Raushel, F. M. (2018). Mechanism and Structure of γ-Resorcylate Decarboxylase. Biochemistry, 57(22), 3167-3175. https://doi.org/10.1021/acs.biochem.7b01213

Mechanism and Structure of γ-Resorcylate Decarboxylase. / Sheng, Xiang; Patskovsky, Yury; Vladimirova, Anna; Bonanno, Jeffrey B.; Almo, Steven C.; Himo, Fahmi; Raushel, Frank M.

In: Biochemistry, Vol. 57, No. 22, 05.06.2018, p. 3167-3175.

Research output: Contribution to journalArticle

Sheng, X, Patskovsky, Y, Vladimirova, A, Bonanno, JB, Almo, SC, Himo, F & Raushel, FM 2018, 'Mechanism and Structure of γ-Resorcylate Decarboxylase', Biochemistry, vol. 57, no. 22, pp. 3167-3175. https://doi.org/10.1021/acs.biochem.7b01213
Sheng, Xiang ; Patskovsky, Yury ; Vladimirova, Anna ; Bonanno, Jeffrey B. ; Almo, Steven C. ; Himo, Fahmi ; Raushel, Frank M. / Mechanism and Structure of γ-Resorcylate Decarboxylase. In: Biochemistry. 2018 ; Vol. 57, No. 22. pp. 3167-3175.
@article{5adfc36faeca4144abbf34d2780d93a9,
title = "Mechanism and Structure of γ-Resorcylate Decarboxylase",
abstract = "γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.",
author = "Xiang Sheng and Yury Patskovsky and Anna Vladimirova and Bonanno, {Jeffrey B.} and Almo, {Steven C.} and Fahmi Himo and Raushel, {Frank M.}",
year = "2018",
month = "6",
day = "5",
doi = "10.1021/acs.biochem.7b01213",
language = "English (US)",
volume = "57",
pages = "3167--3175",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "22",

}

TY - JOUR

T1 - Mechanism and Structure of γ-Resorcylate Decarboxylase

AU - Sheng, Xiang

AU - Patskovsky, Yury

AU - Vladimirova, Anna

AU - Bonanno, Jeffrey B.

AU - Almo, Steven C.

AU - Himo, Fahmi

AU - Raushel, Frank M.

PY - 2018/6/5

Y1 - 2018/6/5

N2 - γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.

AB - γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.

UR - http://www.scopus.com/inward/record.url?scp=85048114129&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85048114129&partnerID=8YFLogxK

U2 - 10.1021/acs.biochem.7b01213

DO - 10.1021/acs.biochem.7b01213

M3 - Article

C2 - 29283551

AN - SCOPUS:85048114129

VL - 57

SP - 3167

EP - 3175

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 22

ER -