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model, it is proposed that conformational changes in these hydrophobic res-
idues upon O
2
binding trigger a conformational change in the distal haem
pocket, which results in conformational changes in the whole molecule of
FixL for the regulation of its autokinase activity.
The X-ray crystal structures of the PAS domain have also been deter-
mined for met, deoxy, O
2
-bound, CO-bound, NO-bound, Im-bound,
MeIm-bound, and CN
-bound
Bj
FixLH (haem-containing PAS domain
of BjFixL) (
Dunham et al., 2003; Gong, Hao, & Chan, 2000; Gong
et al., 1998; Hao, Isaza, Arndt, Soltis, & Chan, 2002; Key & Moffat,
2005
). The overall structures of the core PAS domains are same between
haem-containing PAS domain of
Sm
FixL (
Sm
FixLH) and
Bj
FixLH, though
Sm
FixLH and
Bj
FixLH are a homodimer and a monomer, respectively.
Comparing the structures of deoxy and O
2
-bound
Bj
FixL reveal that a con-
formation of the haem itself is altered upon O
2
binding to the haem
(
Dunham et al., 2003; Gong et al., 2000, 1998; Hao et al., 2002; Key &
Moffat, 2005
). Though the met and deoxy haems are ruffling in
Bj
FixLH,
O
2
binding to the haem causes a flattening of the haem. A similar flattening
of the haem is also observed in CO-, NO-, and CN
-bound haems for
Bj
FixLH (
Fig. 7.3
). While O
2
and CN
inhibit the FixL activity, CO
and NO do not (
Akimoto et al., 2003; Gilles-Gonzalez et al., 2006;
Sousa, Tuckerman, Gondim, Gonzalez, & Gilles-Gonzalez, 2013
). The
degree of flattening upon CO or NO binding is smaller compared with that
upon O
2
or CN
binding. Thus, it partly correlates with the functional reg-
ulation of FixL whether or not the flattening of the haem takes place.
4.1.3 Functional roles of amino acid residues in the haem pocket
Electrostatic interactions network among the haem propionate groups and
surrounding amino acid residues is rearranged upon O
2
binding. A salt bridge
between Arg220, which is located at the C-terminal end of the FG loop, and
the haem propionate in deoxy
Bj
FixLH is lost in oxy
Bj
FixLH. A new salt
bridge is formed between Arg206 and the haem propionate 6 in oxy
Bj
FixLH,
while the side chain of Arg206 is interacting with the main-chain carbonyl
oxygen of Asp212 without interaction with the haem propionate 6 in deoxy
Bj
FixL (
Hao et al., 2002; Key & Moffat, 2005
). Resonance Raman spectros-
copy reveals the reconstruction of salt bridge with the haem propionate
(
Balland et al., 2006
). The R200A
Sm
FixL variant (R206A for
Bj
FixL) shows
the same O
2
-dependent regulation for autophosphorylation, indicating that
the salt bridge interaction between the Arg residue and the haem propionate
