School of Pharmaceutical Sciences, East Campus, Sun Yat-Sen University, Guangzhou 510006, China.
J Struct Biol. 2010 Mar;169(3):304-11. doi: 10.1016/j.jsb.2009.11.008. Epub 2009 Nov 20.
A crystal structure of the putative N-carbamoylsarcosine amidase (CSHase) Ta0454 from Thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35A. CSHases are involved in the degradation of creatinine. Ta0454 shares a similar fold and a highly conserved C-D-K catalytic triad (Cys123, Asp9, and Lys90) with the structures of three cysteine hydrolases (PDB codes 1NBA, 1IM5, and 2H0R). Molecular dynamics (MD) simulations of Ta0454/N-carbamoylsarcosine and Ta0454/pyrazinamide complexes were performed to determine the structural basis of the substrate binding pattern for each ligand. Based on the MD-simulated trajectories, the MM/PBSA method predicts binding free energies of -24.5 and -17.1 kcal/mol for the two systems, respectively. The predicted binding free energies suggest that Ta0454 is selective for N-carbamoylsarcosine over pyrazinamide, and zinc ions play an important role in the favorable substrate bound states.
从嗜酸性热原体中分离出的假定 N-氨甲酰基肌氨酸酰胺酶 (CSHase) Ta0454 的晶体结构通过单波长反常散射法解析，并在 2.35Å 的分辨率下进行了精修。CSHases 参与肌酸酐的降解。Ta0454 与三种半胱氨酸水解酶 (PDB 代码 1NBA、1IM5 和 2H0R) 的结构具有相似的折叠和高度保守的 C-D-K 催化三联体 (Cys123、Asp9 和 Lys90)。对 Ta0454/N-氨甲酰基肌氨酸和 Ta0454/吡嗪酰胺复合物进行分子动力学 (MD) 模拟，以确定每个配体的底物结合模式的结构基础。根据 MD 模拟轨迹，MM/PBSA 方法分别预测两个体系的结合自由能为-24.5 和-17.1 kcal/mol。预测的结合自由能表明 Ta0454 对 N-氨甲酰基肌氨酸的选择性高于吡嗪酰胺，锌离子在有利的底物结合态中发挥重要作用。
