Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6

J Bacteriol. 1999 Jan;181(1):55-62. doi: 10.1128/JB.181.1.55-62.1999.


Sphingomonas paucimobilis SYK-6 is able to grow on a wide variety of dimeric lignin compounds with guaiacyl moieties, which are converted into protocatechuate by the actions of lignin degradation enzymes in this strain. Protocatechuate is a key metabolite in the SYK-6 degradation of lignin compounds with guaiacyl moieties, and it is thought that it degrades to pyruvate and oxaloacetate via the protocatechuate 4,5-cleavage pathway. In a 10.5-kb EcoRI fragment carrying the protocatechuate 4,5-dioxygenase gene (ligAB) (Y. Noda, S. Nishikawa, K. Shiozuka, H. Kadokura, H. Nakajima, K. Yoda, Y. Katayama, N. Morohoshi, T. Haraguchi, and M. Yamasaki. J. Bacteriol. 172:2704-2709, 1990), we found the ligI gene encoding 2-pyrone-4, 6-dicarboxylic acid (PDC) hydrolase. PDC hydrolase is a member of this pathway and catalyzes the interconversion between PDC and 4-carboxy-2-hydroxymuconic acid (CHM). The ligI gene is thought to be transcribed divergently from ligAB and consists of an 879-bp open reading frame encoding a polypeptide with a molecular mass of 32,737 Da. The ligI gene product (LigI), expressed in Escherichia coli, was purified to near-homogeneity and was estimated to be a monomer (31.6 kDa) by gel filtration chromatography. The isoelectric point was determined to be 4.9. The optimum pH for hydrolysis of PDC is 8.5, the optimum pH for synthesis of PDC is 6.0 to 7.5, and the Km values for PDC and CHM are 74 and 49 microM, respectively. LigI activity was inhibited by the addition of thiol reagents, suggesting that the cysteine residue is a catalytic site. LigI is more resistant to metal ion inhibition than the PDC hydrolases of Pseudomonas ochraceae (K. Maruyama, J. Biochem. 93:557-565, 1983) and Comamonas testosteroni (P. J. Kersten, S. Dagley, J. W. Whittaker, D. M. Arciero, and J. D. Lipscomb, J. Bacteriol. 152:1154-1162, 1982). The insertional inactivation of the ligI gene in S. paucimobilis SYK-6 led to the complete loss of PDC hydrolase activity and to a growth defect on vanillic acid; it did not affect growth on syringic acid. These results indicate that the ligI gene is essential for the growth of SYK-6 on vanillic acid but is not responsible for the growth of SYK-6 on syringic acid.

MeSH terms

  • Carboxylic Ester Hydrolases / chemistry
  • Carboxylic Ester Hydrolases / genetics*
  • Carboxylic Ester Hydrolases / metabolism*
  • Cations, Divalent / pharmacology
  • DNA, Bacterial / genetics
  • Escherichia coli / genetics
  • Gene Expression
  • Genes, Bacterial*
  • Hydrogen-Ion Concentration
  • Hydroxybenzoates / metabolism
  • Kinetics
  • Molecular Sequence Data
  • Molecular Weight
  • Mutagenesis, Insertional
  • Protein Conformation
  • Pseudomonas / enzymology*
  • Pseudomonas / genetics*
  • Pseudomonas / growth & development
  • Sequence Analysis, DNA
  • Sequence Deletion
  • Substrate Specificity
  • Sulfhydryl Reagents / pharmacology


  • Cations, Divalent
  • DNA, Bacterial
  • Hydroxybenzoates
  • Sulfhydryl Reagents
  • protocatechuic acid
  • 2-pyrone-4,6-dicarboxylic acid hydrolase
  • Carboxylic Ester Hydrolases

Associated data

  • GENBANK/AB015964