New insights for dinucleotide backbone binding in conserved C5'-H . . . O hydrogen bonds.
Most enzymes that utilize dinucleotide NAD or NADP are known to comprise a glycine-rich loop segment (e.g. the GXGXXG signature motif of Rossman fold) which binds the cofactor's diphosphate moiety. Through analysis of a set of diverse NAD(P)-bound protein structures, we show here that with few exceptions this diphosphate binding is complemented by a second loop segment interacting from a different angle with unconventional yet apparently ubiquitous C-HellipsisO hydrogen bonds formed between C5' methylene of dinucleotide and, primarily, carbonyl oxygen of protein. This finding implicates an important role of C5' in protein-nucleotide recognition.
Chu
P Y
PY
Division of Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
Hwang
M J
MJ
D000818:Animals; D001665:Binding Sites; D006801:Humans; D006859:Hydrogen / Q000737:chemistry*; D009243:NAD / Q000737:chemistry*; D009249:NADP / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
D011506:Proteins; D009243:NAD; D009249:NADP; D006859:Hydrogen