Prediction of the structure of the replication initiator protein DnaA

✍ Scribed by Sigrid Schaper; and Walter Messer

• Publisher: John Wiley and Sons
• Year: 1997
• Tongue: English
• Weight: 196 KB
• Volume: 28
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(199705)28:1<1::aid-prot1>3.0.co;2-k

✦ Synopsis

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 a/b structure,'' containing five a-helices alternating with five b-strands. In our proposed structural model the interior of the core is formed by a parallel b-sheet, whereas the a-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 b-strand. The N-terminal domain (80 aa) is composed of two a-helices, the first of which contains a potential leucine zipper motif for mediating protein-protein interaction, followed by a b-strand and an additional a-helix. The N-terminal domain and the a/b 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 a-helical and contains a potential helixloop-helix motif. DnaA protein does not dimerize in solution; instead, the two longest C-terminal a-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.