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di-AMP, and cyclic di-GMP, while the GGDEF domain possesses a weak
ATPase activity instead of the DGC activity (
Rao et al., 2010
). The
DHH/DHHA1 domain hydrolyzes cyclic di-AMP and cyclic di-GMP to
generate the linear dinucleotides, 5
0
-pApA and 5
0
-pGpG, respectively.
YybT from
Bacillus subtilis
shows the Soret and Q-bands at 412, 533, and
566 nm, and 423, 528, and 557 nm in the ferric and ferrous forms, respec-
tively, though the haem contents of the recombinant YybT are low (ca. 5%)
(
Rao et al., 2011
). These spectral features suggest that the ferric and ferrous
haems in YybT are in a 6-coordinate and low-spin state, though it remains
unknown what residues are the axial ligands of the haem in YybT. As autox-
idation proceeds to produce the ferric form upon the reaction of ferrous
YybT with O
2
, no stable O
2
-bound form of YybT is formed. NO and
CO can be bound to the ferrous YybT to form a 5-coordinate nitrosyl haem
and a 6-coordinate CO-bound haem, respectively (
Rao et al., 2011
).
YybT binds a b-type haem as described earlier. However, amino acid
sequence alignment of the PAS domain of YybT family proteins with the
haem-binding PAS domain of FixL and
Ec
Dos reveals that there is no can-
didate of the axial ligands of the haem in YybT. Secondary structure predic-
tion and structural modelling suggest that the F
a
helix and G
b
strand are
shorter than those of FixL and
Ec
Dos and the FG loop is absent in YybT,
though the same topology is conserved in the PAS domain in YybT
(
Rao et al., 2011
). Very recently, the solution structure of the PAS domain
of YybT from
Geobacillus thermodenitrificans
(
Gt
Yyb) is determined by NMR
to indicate that it adopts the characteristic PAS fold composed of a five-
stranded antiparallel
b
sheet and a few short
a
helices (
Tan et al., 2013
).
It forms a homodimer with the interaction of the central
b
-sheet in an anti-
parallel fashion (
Tan et al., 2013
). As three of the
b
strands and one of the
helices in the PAS domain of
Gt
YybT are shorter than those found in other
typical PAS domains, the PAS domain of
Gt
YybT consists of only 80 resi-
dues. Despite the small size of the domain, it forms a hydrophobic cavity by
backbone and side chains of predominantly non-polar residues, Leu88,
Leu103, Ala104, Phe107, Glu109, Leu112, Leu117, Leu120, Ser121,
Leu124, Leu145, and Phe158 (
Tan et al., 2013
). As expected from the
sequence analyses, there is no residue that can act as the axial ligands of
the haem in this cavity. These results suggest that the haem is bound in this
cavity by hydrophobic interactions.
The catalytic activity of YybT with a substrate of cyclic di-AMP is reg-
ulated by whether or not YybT binds a haem. Apo-YybT shows a higher
activity by 15-fold compared with holo-YybT. The
k
cat
and the
K
m
for
