Biology Reference
In-Depth Information
Hiruma et al. (2007)
propose the following scheme of structural changes
upon ligand dissociation. In the step 1, the interaction between Arg214
(Arg220 in
Bj
FixL) and O
2
is lost upon O
2
dissociation, resulting in the reor-
ientation of Arg214 towards haem propionate 7 to form a salt bridge with it.
The increase in the
n
8 mode intensity corresponds to the formation of the
salt bridge between Arg214 and haem propionate 7. The formation of this
salt bridge will intensify haem doming and thus intensifies the
g
7 band,
which results in the intensity changes of the
g
7,
n
8, and
d
(C
b
C
c
C
d
) modes.
In the step 2, spectral changes are observed for the
d
(C
b
C
c
C
d
) band in a
timescale of 1-10
m
s, which is caused by the movement of Ile209 and
Ile210 in the distal haem pocket. The main-chain amide of Ile209 is hydro-
gen bonded to haem propionate 6 in the ligand-bound forms, but not in the
deoxy form. The spectral changes in the step 2 will correspond to recon-
struction of this hydrogen-bond interaction. For both CO and O
2
dissoci-
ation, relaxations to the equilibrium deoxy form are not complete after 2 ms
(
Hiruma et al., 2007
). The changes in the
g
7,
n
8, and
d
(C
b
C
c
C
d
) modes will
correspond to changes in the extent of haem doming and interactions
between the amino acid residues in the FG loop and the haem propionates
in the step 3.
4.1.6 A structural model of FixL/FixJ complex
Though the structures of the PAS domain of FixL are reported, the structure
of full-length FixL is not solved yet. The structures of FixL in the full-length
and FixL/FixJ complex are required to unveil the detailed molecular mech-
anisms of signal transductions in the FixL/FixJ two-component system.
Yamada et al. (2009)
report the structure of the complex of the PAS-
containing sensory histidine kinase (ThkA) and its cognate response regula-
tor (TrrA) in the two-component signal transduction system of
Thermotoga
maritima
, which would be a good model of the FixL/FixJ system. They con-
struct a structural model of ThkA/TrrA complex by fitting the structures of
the isolated domains of ThkA and TrrA that are determined with high res-
olution (1.5-1.9
˚
) into the electron density map of the ThkA/TrrA com-
plex at a resolution of 3.6
˚
(
Fig. 7.5
).
ThkA consists of the PAS, dimerization (DHp), and kinase catalytic (CA)
domains. The domain organisation is conserved between FixL and ThkA,
though the PAS domain in ThkA contains no prosthetic group. The
b
3
in the ThkA PAS domain forms an interdomain, antiparallel
b
sheet with
the
b
6 in the CA domain of ThkA via four main-chain hydrogen bonds
(
Yamada et al., 2009
). The
b
3 in the ThkA PAS domain is located in the
