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  4. Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis
 
research article

Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis

Dal Peraro, M.  
•
Vila, A. J.
•
Carloni, P.
2003
Inorg Chem

The determination of the protonation state of enzyme active sites may be crucial for the investigation of their mechanism of action. In the bizinc beta-lactamase family of enzymes, no consensus has been reached on the protonation state of a fully conserved amino acid present in the active site, Asp120. To address this issue, we carry out here density functional theory (DFT) calculations on large models (based on Bacteroides fragilis X-ray structure) which include the metal coordination polyhedron and groups interacting with it. Our calculations suggest that Asp120 is ionized. The relevance of this finding for site-directed mutagenesis experiments on the 120 position and on the mechanism of action is discussed.

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Type
research article
DOI
10.1021/ic026059j
Author(s)
Dal Peraro, M.  
Vila, A. J.
Carloni, P.
Date Issued

2003

Published in
Inorg Chem
Volume

42

Issue

14

Start page

4245

End page

7

Subjects

Aspartic Acid/*chemistry

•

Bacteroides fragilis/*enzymology

•

Binding Sites

•

Catalysis

•

Computational Biology

•

Models

•

Molecular

•

Molecular Conformation

•

Mutagenesis

•

Site-Directed

•

Protons

•

beta-Lactamases/*chemistry/genetics

Note

International School for Advanced Studies, SISSA and INFM-DEmocritos MOdeling Center for Research in aTOmistic Simulation, via Beirut 2-4, 34014 Trieste, Italy.

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
UPDALPE  
Available on Infoscience
April 28, 2008
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/23504
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