A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis

Yamei Yu, Yu He Liang, Erik Brostromer, Jun Min Quan, Santosh Panjikar, Yu Hui Dong, Xiao Dong Su

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Imidazolonepropionase (EC catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-L-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-Å resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small β-sandwich domain. The TIM barrel domain is quite similar to the members of the α/β barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 Å away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.

Original languageEnglish
Pages (from-to)36929-36936
Number of pages8
JournalJournal of Biological Chemistry
Issue number48
Publication statusPublished - 1 Dec 2006
Externally publishedYes

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