Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach.
Consensus sequence patterns for beta-alpha-beta folds binding FAD, NAD and GTP were constructed on the basis of 11 steric and physicochemical properties. These property patterns permit detection and distinction of the respective nucleotide-binding sites on the basis of amino acid sequence analysis alone. The SWISS-PROT database (release 9) was screened with the three calculated patterns, and nucleotide-binding sites identified are presented. They correspond to existing structure data (if known). For the detected sequence segments we are able to predict the beta-alpha-beta motif as well as the respective binding sites. For some of the proteins so detected a nucleotide-binding capacity has not previously been reported.
Bork
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Department of Biomathematics, Central Institute of Molecular Biology, Academy of Sciences of German Democratic Republic, Berlin-Buch.
Grunwald
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D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D005182:Flavin-Adenine Dinucleotide / Q000235:genetics; D006160:Guanosine Triphosphate / Q000235:genetics; D007256:Information Systems; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009243:NAD / Q000235:genetics; D009711:Nucleotides / Q000235:genetics*; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D013329:Structure-Activity Relationship
D000596:Amino Acids; D009711:Nucleotides; D009243:NAD; D005182:Flavin-Adenine Dinucleotide; D006160:Guanosine Triphosphate