Download MendeleyCrystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.
Luo, H.B., Zheng, H., Zimmerman, M.D., Chruszcz, M., Skarina, T., Egorova, O., Savchenko, A., Edwards, A.M., Minor, W.(2010) J Struct Biol 169: 304-311
- PubMed: 19932181
- DOI: https://doi.org/10.1016/j.jsb.2009.11.008
- Primary Citation of Related Structures:
3EEF - PubMed Abstract:
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.
Organizational Affiliation:
School of Pharmaceutical Sciences, East Campus, Sun Yat-Sen University, Guangzhou 510006, China.
