PROTEIN MOTIFS .9. THE NICOTINAMIDE DINUCLEOTIDE BINDING MOTIF - A COMPARISON OF NUCLEOTIDE-BINDING PROTEINS

Classical nicotinamide adenine dinucleotide (NAD(+)) binding proteins contain a beta alpha beta alpha beta unit. By comparing 14 such protei ns, it is observed that an additional beta strand associates with this unit to form the ''core'' topology, the minimum structure necessary t o bind cofactor. Although the overall topologies of the cofactor bindi ng domains of nicotinamide binding proteins vary, they all contain at least the core topology, The first 30-35 amino acids of the core topol ogy, called the ''fingerprint'' region, are diagnostic for the presenc e of a dinucleotide binding fold, There are four characteristics of th is fingerprint region: 1) a phosphate binding consensus sequence, GXGX XG, 2) six positions usually occupied by small hydrophobic amino acids , 3) a conserved, negatively charged residue (Glu or Asp) at the end o f the second beta strand of the fingerprint region, and 4) a conserved positively charged residue (Arg or Lys) at the beginning of the first beta strand of the fingerprint region, The core topologies of the cla ssical nicotinamide binding proteins overlap well with root mean squar ed deviations of main chain atoms ranging from 0.7 to 4.7 Angstrom. A conserved interaction (found in 8 of the 12 classical nicotinamide bin ding proteins studied) between the cofactor and the protein is a hydro gen bond between the pyrophosphate oxygen of NAD(P)(+) and the carboxy -terminal glycine of the phosphate binding helix, the first alpha heli x of the beta alpha beta alpha beta unit. The classical nicotinamide b inding proteins all bind their cofactor in the same location and orien tation, with the cofactor itself adopting a similar extended conformat ion in every structure. Although observed less frequently than the cla ssical fold, numerous nonclassical folding patterns are also used by p roteins that bind NAD(P)(+).