Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1: A novel subset of amidohydrolases and insights into the enzyme mechanism

Shwu Huey Liaw, Shen Jia Chen, Tzu Ping Ko, Cheng Sheng Hsu, Chun Jung Chen, Andrew H.J. Wang, Ying Chieh Tsai

Research output: Contribution to journalArticlepeer-review

57 Citations (Scopus)

Abstract

D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino acids. We report here the first D-aminoacylase crystal structure from A. faecalis at 1.5-Å resolution. The protein comprises a small β-barrel, and a catalytic (βα)s-barrel with a 63-residue insertion. The enzyme structure shares significant similarity to the α/β-barrel amidohydrolase superfamily, in which the β-strands in both barrels superimpose well. Unexpectedly, the enzyme binds two zinc ions with widely different affinities, although only the tightly bound zinc ion is required for activity. One zinc ion is coordinated by Cys96, His220, and His250, while the other is loosely chelated by His67, His69, and Cys96. This is the first example of the metal ion coordination by a cysteine residue in the superfamily. Therefore, D-aminoacylase defines a novel subset and is a mononuclear zinc metalloenzyme but containing a binuclear active site. The preferred substrate was modeled into a hydrophobic pocket, revealing the substrate specificity and enzyme catalysis. The 63-residue insertion containing substrate-interacting residues may act as a gate controlling access to the active site, revealing that the substrate binding would induce a closed conformation to sequester the catalysis from solvent.

Original languageEnglish
Pages (from-to)4957-4962
Number of pages6
JournalJournal of Biological Chemistry
Volume278
Issue number7
DOIs
Publication statusPublished - Feb 14 2003
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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