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Figure 6.
Figure 6. Proposed Sda Binding Site and Mechanism of
Action(A) Alignment of EnvZ with KinA, B, and C. Numbering
refers to KinA. Residues that are identical or conservatively
substituted in at least three of the four sequences are
highlighted in yellow and orange, respectively. The
experimentally determined secondary structure of the EnvZ DHp
(Tomomori et al., 1999) and catalytic (Tanaka et al., 1998)
domains is given below the alignment. Linker regions are
demarcated by red lines. The percentage identity (I) and
similarity (S) relative to KinA is indicated at the end of each
sequence.(B) Modeled structure of the EnvZ autokinase domain
(PDB file 1NJV) (Cai et al., 2003). Domains and linkers are
color-coded to match the sequence alignment in (A). In (B)–(D)
the side chain of the phosphorylatable His is colored orange.(C)
Schematic of the Spo0F-Spo0B cocrystal structure (PDB file
1F51). Only the N-terminal four-helix bundle of the Spo0B dimer
is shown; the C-terminal α/β domains have been omitted for
clarity. The side chain of the active-site Asp residue in Spo0F
is shown in red.(D) Schematic of the structure of the EnvZ DHp
domain (PDB file 1JOY). Highlighted in red is the OmpR binding
site determined by NMR chemical shift mapping (Tomomori et al.,
1999).(E) Alignment of KinA^383–460 with Spo0B. The secondary
structure of the four-helix bundle of Spo0B is indicated below
the sequences. Residues in Spo0B that contact Spo0F (Zapf et
al., 2000) are indicated by red circles, and the active-site
His residues are denoted by an asterisk (His405 in KinA, His30
in Spo0B). The predicted Spo0F binding site on KinA and the area
available for Sda binding are indicated above the sequences.(F)
Schematic of the closed conformation of the KinA autokinase
domain based on the EnvZ model structure. The two monomers are
shown in orange and blue, the phosphorylatable His405 is
depicted as a green circle, and the approximate location of the
ATP binding site on the catalytic domain is indicated. The
predicted Spo0F binding site and the area available for Sda
binding are indicated.(G and H) Two alternative models of the
mechanism of Sda action. Sda could lodge under the linker region
at the top of the DHp domain (G) or bind exclusively to the
linker region (H). Either orientation could explain why Sda
enhances KinA dimerization (see text for details).
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