2BB0

Structure of Imidazolonepropionase from Bacillus subtilis

Summary for 2BB0

• Entry DOI: 10.2210/pdb2bb0/pdb
• Descriptor: Imidazolonepropionase, ACETATE ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: tim barrel, hydrolase
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm : P42084
• Total number of polymer chains: 2
• Total formula weight: 91480.55

Authors

Liang, Y.H.,Yu, Y.,Su, X.D. (deposition date: 2005-10-16, release date: 2006-09-26, Last modification date: 2024-03-13)

Primary citation

Yu, Y.,Liang, Y.H.,Brostromer, E.,Quan, J.M.,Panjikar, S.,Dong, Y.H.,Su, X.D.
A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis
J.Biol.Chem., 281:36929-36936, 2006

PubMed Abstract: Imidazolonepropionase (EC 3.5.2.7) 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-A 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 beta-sandwich domain. The TIM barrel domain is quite similar to the members of the alpha/beta 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 A 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.

PubMed: 16990261
DOI: 10.1074/jbc.M607703200

Experimental method

X-RAY DIFFRACTION (2 Å)