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Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis
Journal article   Open access   Peer reviewed

Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis

Phaneeswara-Rao Kommoju, Robert C Bruckner, Patricia Ferreira and Marilyn Schuman Jorns
Biochemistry (Easton), v 48(29), pp 6951-6962
28 Jul 2009
DOI: https://doi.org/10.1021/bi9006918
PMID: 19530706
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https://doi.org/10.1021/bi9006918View
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Abstract

Molecular Probes Catalytic Domain Biocatalysis Models, Molecular DNA Primers Amino Acid Oxidoreductases - metabolism Cyclization Mutagenesis Spectrum Analysis - methods Base Sequence Amino Acid Oxidoreductases - chemistry Aminoglycosides - biosynthesis Kinetics
NikD catalyzes a remarkable aromatization reaction that converts piperideine 2-carboxylate (P2C) to picolinate, a key component of the nonribosomal peptide in nikkomycin antibiotics. The enzyme exhibits a FAD-Trp355 charge-transfer band at weakly alkaline pH that is abolished upon protonation of an unknown ionizable residue that exhibits a pK(a) of 7.3. Stopped-flow studies of the reductive half-reaction with wild-type nikD and P2C show that the enzyme oxidizes the enamine tautomer of P2C but do not distinguish among several possible paths for the initial two-electron oxidation step. Replacement of Glu101 or Asp276 with a neutral residue does not eliminate the ionizable group, although the observed pK(a) is 1 or 2 pH units higher, respectively, compared with that of wild-type nikD. Importantly, the mutations cause only a modest decrease (<5-fold) in the observed rate of oxidation of P2C to dihydropicolinate. The results rule out the only possible candidates for a catalytic base in the initial two-electron oxidation step. This outcome provides compelling evidence that nikD oxidizes the bond between N(1) and C(6) in the enamine tautomer of P2C, ruling out alternative paths that require an active site base to mediate the oxidation of a carbon-carbon bond. Because the same restraint applies to the second two-electron oxidation step, the dihydropicolinate intermediate must be converted to an isomer that contains an oxidizable carbon-nitrogen bond. A novel role is proposed for reduced FAD as an acid-base catalyst in the isomerization of dihydropicolinate.

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Web of Science research areas
Biochemistry & Molecular Biology
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