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PEDS Advance Access originally published online on April 28, 2004
Protein Engineering Design and Selection 2004 17(3):223-234; doi:10.1093/protein/gzh033
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© 2004 Oxford University Press

Cluster analysis of water molecules in alanine racemase and their putative structural role

Gabriela Mustata1,2 and James M. Briggs1,3

1Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA 2Present address: Emisphere Technologies, Inc., Tarrytown, NY 10591, USA

3 To whom correspondence should be addressed. e-mail: jbriggs{at}uh.edu

Conservation of water molecules was identified by a cluster analysis of seven crystal structures of alanine racemase from Bacillus stearothermophilus. A total of 47 clusters of consensus water sites were determined and found to be highly localized, as indicated by their low mobilities. These clusters are located in the region of the active sites as well as at the interface between the N-terminal domain (the {alpha}/ß-barrel) of the first monomer and the C-terminal domain of the second monomer. The clusters located at the dimer interface form extensive hydrogen-bonding networks linked to the protein backbone. These water-mediated hydrogen bonds, and also all hydrogen-bonding interactions at the dimer interface, were monitored during a 2 ns molecular dynamics simulation and showed that when the inhibitor propionate was bound to the enzyme, some of these interactions were disrupted. The data we present here indicate that the consensus water sites identified at the interface between the two monomers of alanine racemase may play a structural role, which is to maintain and stabilize the alanine racemase dimer. A second role might be to supply the active site continuously with water molecules in order to allow rapid equilibration of active site protons with the solvent.

Received December 4, 2003; revised March 21, 2004; accepted March 31, 2004 Edited by Brian Matthews


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