Structure and catalytic mechanism of LigI: Insight into the amidohydrolase enzymes of cog3618 and lignin degradation

Merlin Eric Hobbs, Vladimir Malashkevich, Howard J. Williams, Chengfu Xu, J. Michael Sauder, Stephen K. Burley, Steven C. Almo, Frank M. Raushel

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Abstract

LigI from Sphingomonas paucimobilis catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to 4-oxalomesaconate and 4-carboxy-2- hydroxymuconate in the degradation of lignin. This protein is a member of the amidohydrolase superfamily of enzymes. The protein was expressed in Escherichia coli and then purified to homogeneity. The purified recombinant enzyme does not contain bound metal ions, and the addition of metal chelators or divalent metal ions to the assay mixtures does not affect the rate of product formation. This is the first enzyme from the amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity. The kinetic constants for the hydrolysis of PDC are 340 s-1 and 9.8 × 106 M -1 s-1 (kcat and kcat/Km, respectively). The pH dependence on the kinetic constants suggests that a single active site residue must be deprotonated for the hydrolysis of PDC. The site of nucleophilic attack was determined by conducting the hydrolysis of PDC in 18O-labeled water and subsequent 13C nuclear magnetic resonance analysis. The crystal structures of wild-type LigI and the D248A mutant in the presence of the reaction product were determined to a resolution of 1.9 Å. The C-8 and C-11 carboxylate groups of PDC are coordinated within the active site via ion pair interactions with Arg-130 and Arg-124, respectively. The hydrolytic water molecule is activated by the transfer of a proton to Asp-248. The carbonyl group of the lactone substrate is activated by electrostatic interactions with His-180, His-31, and His-33.

Original languageEnglish (US)
Pages (from-to)3497-3507
Number of pages11
JournalBiochemistry
Volume51
Issue number16
DOIs
Publication statusPublished - Apr 24 2012

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ASJC Scopus subject areas

  • Biochemistry

Cite this

Hobbs, M. E., Malashkevich, V., Williams, H. J., Xu, C., Sauder, J. M., Burley, S. K., ... Raushel, F. M. (2012). Structure and catalytic mechanism of LigI: Insight into the amidohydrolase enzymes of cog3618 and lignin degradation. Biochemistry, 51(16), 3497-3507. https://doi.org/10.1021/bi300307b