3EEF

Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum

Summary for 3EEF

• Entry DOI: 10.2210/pdb3eef/pdb
• Descriptor: N-carbamoylsarcosine amidase related protein, ZINC ION (3 entities in total)
• Functional Keywords: n-carbamoylsarcosine amidase, protein, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, hydrolase
• Biological source: Thermoplasma acidophilum
• Total number of polymer chains: 2
• Total formula weight: 41718.01

Authors

Luo, H.-B.,Zheng, H.,Chruszcz, M.,Zimmerman, M.D.,Skarina, T.,Egorova, O.,Savchenko, A.,Joachimiak, A.,Minor, W.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2008-09-04, release date: 2008-09-16, Last modification date: 2024-11-13)

Primary citation

Luo, H.B.,Zheng, H.,Zimmerman, M.D.,Chruszcz, M.,Skarina, T.,Egorova, O.,Savchenko, A.,Edwards, A.M.,Minor, W.
Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.
J.Struct.Biol., 169:304-311, 2010

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.

PubMed: 19932181
DOI: 10.1016/j.jsb.2009.11.008

Experimental method

X-RAY DIFFRACTION (2.35 Å)