How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.
Sci Rep
; 4: 7453, 2014 Dec 12.
Article
en En
| MEDLINE
| ID: mdl-25503313
ABSTRACT
Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Proteínas Bacterianas
/
Agua
/
Amidohidrolasas
Idioma:
En
Revista:
Sci Rep
Año:
2014
Tipo del documento:
Article
País de afiliación:
China