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Figure 1.
FIGURE 1. Structural models of DnaA oligomers and tmaDnaA
mutants. A, crystal structure of tmaDnaA AAA^+ domain. The
crystal structure of tmaDnaA AAA^+ domain bound to ADP was
solved by molecular replacement. The A. aeolicus DnaA AAA^+
domain structure (22) was used as a search model. The subdomains
IIIa and IIIb within AAA^+ domain are depicted as a ribbon model
in different colors. B, structure comparison. Structures of
AAA^+ domain of tmaDnaA and A. aeolicus DnaA, colored purple and
cyan, respectively, were superimposed for subdomain IIIa.
Structures are shown in a frame model. C, a ring model structure
of tmaDnaA. A hexameric ring model was constructed using the
determined structure of tmaDnaA AAA^+ domain. Each protomer is
colored differently. The amino acid residues of Val-176,
Met-179, Lys-180, Lys-209, and Gly-211 are exposed on the pore
surface of the ring and are colored in red. For i–vi, see
panel F. D, a spiral filament model structure of tmaDnaA. A
spiral filament model was constructed using the structure of
tmaDnaA AAA^+ domain, based on the spiral filament structure of
the A. aeolicus DnaA AAA^+ domain (37). The model filament is
shown viewed down the helical axis (top), as well as
perpendicularly to the axis (bottom). Each protomer is colored
differently. The amino acid residues described above are also
exposed on the pore surface of the spiral filament and are
colored red. E, the pore surfaces of the tmaDnaA ring and spiral
filament. Three consecutive molecules of tmaDnaA within the ring
(C) and spiral (D) models are shown. The amino acid residues
described above and analyzed in this study are colored red and
indicated. F, amino acid sequences, including the putative pore
region of representative DnaA orthologs. i–vi correspond to E.
coli DnaA residues of Val-211, Leu-214, Gln-215, Lys-223,
Lys-243, and Arg-245, respectively. Residues corresponding to
these are highlighted in yellow for hydrophobic residues or in
purple for basic residues. The secondary structures of A.
aeolicus DnaA (helix  3- 6) are also shown (22).
Ecoli, Escherichia coli; Thema, Thermotoga maritima; Aquae,
Aquifex aeolicus; Helph, Helicobacter pylori; Bacsu, Bacillus
subtilis; Myctu, Mycobacterium tuberculosis; Chlmu, and
Chlamydia muridarum. G, tma-oriC unwinding assay. The indicated
amounts of wild-type (WT) or mutant tmaDnaA proteins were
incubated at 48 °C for 10 min in the presence of pOZ14 (200
fmol), which bears the tma-oriC, followed by digestion with P1
nuclease and AlwNI.
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