Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes.
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.
Babor
Mariana
M
Departament of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel. mariana.babor@weizmann.ac.il
Sobolev
Vladimir
V
Edelman
Marvin
M
D000244:Adenosine Diphosphate / Q000737:chemistry*; D000255:Adenosine Triphosphate / Q000737:chemistry*; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D008024:Ligands; D011506:Proteins; D014867:Water; D005182:Flavin-Adenine Dinucleotide; D000244:Adenosine Diphosphate; D012266:Ribose; D000255:Adenosine Triphosphate