Prediction of the structure of the replication initiator protein DnaA

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 α/β structure,” containing five α‐helices alternating with five β‐strands. In our proposed structural model the interior of the core is formed by a parallel β‐sheet, whereas the α‐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 β‐strand. The N‐terminal domain (80 aa) is composed of two α‐helices, the first of which contains a potential leucine zipper motif for mediating protein‐protein interaction, followed by a β‐strand and an additional α‐helix. The N‐terminal domain and the α/β 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 α‐helical and contains a potential helix‐loop‐helix motif. DnaA protein does not dimerize in solution; instead, the two longest C‐terminal α‐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. © 1997 Wiley‐Liss Inc.