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Research Article

Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: A special subgroup of the type III extradiol dioxygenases

¹ Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China
² Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, China
³ MacCHESS, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York 14853, USA

(RECEIVED November 13, 2005; FINAL REVISION December 7, 2005; ACCEPTED December 13, 2005)

3-Hydroxyanthranilic acid 3,4-dioxygenase (3HAO) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA) receptors and the precursor of NAD⁺ biosynthesis. The crystal structure of 3HAO from S. cerevisiae at 2.4 Å resolution shows it to be a member of the functionally diverse cupin superfamily. The structure represents the first eukaryotic 3HAO to be resolved. The enzyme forms homodimers, with two nickel binding sites per molecule. One of the bound nickel atoms occupies the proposed ferrous-coordinated active site, which is located in a conserved double-strand -helix domain. Examination of the structure reveals the participation of a series of residues in catalysis different from other extradiol dioxygenases. Together with two iron-binding residues (His49 and Glu55), Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101, Gln59, and the substratebinding hydrophobic pocket are crucial for substrate specificity. Structure comparison with 3HAO from Ralstonia metallidurans reveals similarities at the active site and suggests the same catalytic mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence comparison, we suggest that bicupin of human 3HAO is the first example of evolution from a monocupin dimer to bicupin monomer in the diverse cupin superfamilies. Based on the model of the substrate HAA at the active site of Y3HAO, we propose a mechanism of catalysis for 3HAO.

Keywords: X-ray crystallography; kynurenine pathway; extradiol dioxygenase; cupin superfamily; 2-His-1-carboxylate facial triad; MAD; 3-hydroxyanthranilic acid 3,4-dioxygenase

Abbreviations: Y3HAO, 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae; RM3HAO, 3-hydroxyanthranilic acid 3,4-dioxygenase from Ralstonia metallidurans; HAA, 3-hydroxyanthranilate; QUIN, quinolinic acid; NMDA, N-methyl-D-aspartate; NAD⁺, nicotinamide adenine dinucleotide; AMPA, -amino-3- hydroxy-5-methyl-isoxazole; 4A3HBA23D, 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. 10d; HPPD, 4-hydroxyphenylpyruvate dioxygenase; HGO, human homogentisate dioxygenase; BphC, 2,3-dihydroxybiphenyl 1,2-dioxygenase from Pseudomonas sp. strain KKS102; MAD, multiple wavelength anomalous dispersion; EC, enzyme classification.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051967906

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