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.

[1]  J. Walker,et al.  Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold. , 1982, The EMBO journal.

[2]  W R Taylor,et al.  Pattern matching methods in protein sequence comparison and structure prediction. , 1988, Protein engineering.

[3]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[4]  G. Schulz,et al.  Structural relationship between glutathione reductase and lipoamide dehydrogenase. , 1984, Journal of molecular biology.

[5]  R H Lathrop,et al.  Prediction of a common structural domain in aminoacyl-tRNA synthetases through use of a new pattern-directed inference system. , 1987, Biochemistry.

[6]  Anders Liljas,et al.  2 Evolutionary and Structural Relationships among Dehydrogenases , 1975 .

[7]  R. Wierenga,et al.  INTERACTION OF PYROPHOSPHATE MOIETIES WITH ALPHA-HELIXES IN DINUCLEOTIDE BINDING-PROTEINS , 1985 .

[8]  Nigel S. Scrutton,et al.  Redesign of the coenzyme specificity of a dehydrogenase by protein engineering , 1990, Nature.

[9]  W R Taylor,et al.  The predicted secondary structures of the nucleotide-binding sites of six cation-transporting ATPases lead to a probable tertiary fold. , 1989, European journal of biochemistry.

[10]  A. Bairoch,et al.  Sequence patterns in protein kinases , 1988, Nature.

[11]  D. Eisenberg,et al.  Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. , 1983, Journal of molecular biology.

[12]  D. Leader,et al.  Identification of protein kinases by computer , 1988, Nature.

[13]  T. Hunter,et al.  The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. , 1988, Science.

[14]  H. Berendsen,et al.  The α-helix dipole and the properties of proteins , 1978, Nature.

[15]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[16]  P. Terpstra,et al.  Prediction of the Occurrence of the ADP-binding βαβ-fold in Proteins, Using an Amino Acid Sequence Fingerprint , 1986 .

[17]  P Bork,et al.  Recognition of functional regions in primary structures using a set of property patterns , 1989, FEBS letters.

[18]  M. Sternberg,et al.  Modelling the ATP‐binding site of oncogene products, the epidermal growth factor receptor and related proteins , 1984, FEBS letters.

[19]  Janet M. Thornton,et al.  Structural and sequence patterns in the loops of βαβ units , 1987 .

[20]  W. Möller,et al.  Phosphate‐binding sequences in nucleotide‐binding proteins , 1985, FEBS letters.

[21]  V. Lim.  Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. , 1974, Journal of molecular biology.

[22]  W. Merrick,et al.  GTP-binding domain: three consensus sequence elements with distinct spacing. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[23]  P Argos,et al.  Homologies and anomalies in primary structural patterns of nucleotide binding proteins. , 1985, European journal of biochemistry.

[24]  F. Jurnak.  Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. , 1985, Science.

[25]  T. Tsuzuki,et al.  Cloning and sequence analysis of cDNAs encoding mammalian mitochondrial malate dehydrogenase. , 1987, Biochemistry.

[26]  Wim G. J. Hol,et al.  The role of the α-helix dipole in protein function and structure , 1985 .

[27]  H. Jörnvall,et al.  Extended superfamily of short alcohol‐polyol‐sugar dehydrogenases: structural similarities between glucose and ribitol dehydrogenases , 1984, FEBS letters.

[28]  W. Taylor,et al.  Identification of protein sequence homology by consensus template alignment. , 1986, Journal of molecular biology.

[29]  A. Mildvan,et al.  ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[30]  W. Kabsch,et al.  Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation , 1989, Nature.

[31]  Michael G. Rossmann,et al.  Chemical and biological evolution of a nucleotide-binding protein , 1974, Nature.

[32]  A. Mclachlan.  Gene duplication and the origin of repetitive protein structures. , 1987, Cold Spring Harbor symposia on quantitative biology.

[33]  Israel Hanukoglu,et al.  cDNA sequence of adrenodoxin reductase. Identification of NADP-binding sites in oxidoreductases. , 1989, European journal of biochemistry.

[34]  Wim G. J. Hol,et al.  Predicted nucleotide-binding properties of p21 protein and its cancer-associated variant , 1983, Nature.