Conserved Positions for Ribose Recognition: Importance of Water Bridging Interactions Among ATP, ADP and FAD-protein Complexes

Author: Babor M.   Sobolev V.   Edelman M.  

Publisher: Academic Press

ISSN: 0022-2836

Source: Journal of Molecular Biology, Vol.323, Iss.3, 2002-10, pp. : 523-532

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Abstract

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand–protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein–ligand complexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved position. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose–protein complexes.© 2002 Elsevier Science Ltd

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