Biology Reference
In-Depth Information
5.2.5 Acetobacter xylinum phosphodiesterase A1
The phosphodiesterase A1 (
Ax
PDEA1) of
Gluconacetobacter xylinus
(formerly
Acetobacter xylinum
) plays an important role for the regulation of bacterial cel-
lulose synthesis, which consists of the N-terminal haem-containing PAS and
C-terminal PDE domains (
Chang et al., 2001
).
Ax
PDEA1 catalyses hydro-
lysis of cyclic di-GMP to 5
0
-pGpG. The enzymatic activity of O
2
-bound
Ax
PDEA1 is about one-third compared with that of ferrous
Ax
PDEA1,
indicating that the haem-containing PAS domain regulates the biological
function of
Ax
PDEA1 via O
2
binding to the haem. The PAS domains of
Ax
PDEA1, FixL, and
Ec
Dos are
>
30% identical in amino acid sequence
and the proximal His to the haem is conserved at the corresponding posi-
tions among these PAS domains (
Chang et al., 2001
).
Resonance Raman spectroscopy reveals that the ferric haem in the PAS
domain of
Ax
PDEA1 is a mixture of 6-coordinate, low-spin and
5-coordinate, high-spin states and that the ferrous haem is a 5-coordinate,
high-spin state (
Tomita et al., 2002
). While the spectral properties of ferric
Ax
PDEA1 are similar to those of ferric
Ec
Dos, ferrous
Ax
PDEA1 shows dif-
ferent properties from those of
Ec
Dos. The ferrous haem in
Ax
PDEA1 is a
5-coordinate state, but it is a 6-coordinate state in EcDos. Thus, O
2
is bound
to a vacant distal site of the ferrous haem in
Ax
PDEA1 without any ligand
exchange unlike
Ec
Dos. These differences suggest different mechanisms of
O
2
-dependent signal transductions between
Ax
PDEA1 and
Ec
Dos.
The PAS domain of
Ax
PDEA1 (
Ax
PDEA1H) shows higher
k
on
(6.6
m
M
1
s
1
) and
k
off
(77 s
1
) values for O
2
binding and dissociation,
respectively, compared with FixL and
Ec
Dos. The autoxidation rate of
Ax
PDEA1 is slowest (
>
12 h of the half-life for the oxy form) among
haem-containing PAS (
Chang et al., 2001
). These properties of
Ax
PDEA1
would be caused by structural differences around the haem or/and differ-
ences in flexibility of the haem pocket, but detail mechanisms remain to
be elucidated.
5.3. A haem-sensing PAS domain regulates the PDE activity
of YybT
YybT family proteins are widely distributed among
Staphylococcus aureus
,
Strep-
tococcus mutans
,and
Listeria monocytogenes
, which contain two N-terminal
transmembrane helices and three predicted protein domains, a putative
PAS domain, a highly degenerate GGDEF domain, and a DHH/DHHA1
domain (
Rao, Ji, Soehano, & Liang, 2011
). The C-terminal DHH/DHHA1
domain exhibits PDE activity towards
the cyclic dinucleotides, cyclic
