Local structure investigation of the active site of the imidazolonepropionase from Bacillus subtilis by XANES spectroscopy and ab initio calculations.
Imidazolonepropionase is an important enzyme that plays a crucial role in the degradation of the histidine in mammals and bacteria. In this contribution a detailed structural investigation is presented of the imidazolonepropionase from Bacillus subtilis at the zinc site by X-ray absorption near-edge structure (XANES) spectroscopy combining experimental data with ab initio calculation in the framework of the multiple-scattering theory. The resolved local structure leads to a modification of the data set in the Protein Data Bank (PDB) (PDB code 2BB0). Actually, data suggest that the carboxyl of the Asp324 moves far away from the zinc ion at the center, while the water molecule and the nearest-neighbor histidines move towards it. This new conformation and the occurrence of a short water-to-zinc bond length support the nucleophilic attack catalytic mechanism proposed for this enzyme.
Yang
Feifei
F
Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
Chu
Wangsheng
W
Yu
Meijuan
M
Wang
Yu
Y
Ma
Sixuan
S
Dong
Yuhui
Y
Wu
Ziyu
Z
D000581:Amidohydrolases / Q000737:chemistry*; D001412:Bacillus subtilis / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D013057:Spectrum Analysis; D014965:X-Rays; D015032:Zinc / Q000737:chemistry
D001426:Bacterial Proteins; D000581:Amidohydrolases; C092896:imidazolonepropionase, Bacillus subtilis; D015032:Zinc