title: Prediction of the structure of the replication initiator protein DnaA.
abstract: The secondary structure of DnaA protein and its interaction with DNA and ribonucleotides has been predicted using biochemical, biophysical techniques, and prediction methods based on multiple-sequence alignment and neural networks. The core of all proteins from the DnaA family consists of an "open twisted alpha/beta structure," containing five alpha-helices alternating with five beta-strands. In our proposed structural model the interior of the core is formed by a parallel beta-sheet, whereas the alpha-helices are arranged on the surface of the core. The ATP-binding motif is located within the core, in a loop region following the first beta-strand. The N-terminal domain (80 aa) is composed of two alpha-helices, the first of which contains a potential leucine zipper motif for mediating protein-protein interaction, followed by a beta-strand and an additional alpha-helix. The N-terminal domain and the alpha/beta core region of DnaA are connected by a variable loop (45-70 aa); major parts of the loop region can be deleted without loss of protein activity. The C-terminal DNA-binding domain (94 aa) is mostly alpha-helical and contains a potential helix-loop-helix motif. DnaA protein does not dimerize in solution; instead, the two longest C-terminal alpha-helices could interact with each other, forming an internal "coiled coil" and exposing highly basic residues of a small loop region on the surface, probably responsible for DNA backbone contacts.
authors.affiliation: Max-Planck-Institut für molekulare Genetik, Berlin, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Schaper
authors.forename: W
authors.initials: W
authors.lastname: Messer
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D002850:Chromatography, Gel; D002942:Circular Dichroism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D005816:Genetic Complementation Test; D008956:Models, Chemical; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria