|
Figure 4.
Figure 4. Comparison of the ligand-binding pockets of the
human and C. tropicalis hydratase 2 subunits. (a) Electrostatic
surface potentials of the HsMFE-2(dDhSCP-2LD) ligand-binding
pocket. The positively and negatively charged regions are
colored blue and red, respectively. The residues suggested to
interact with the CoA moiety of the fatty enoyl-CoA substrate
are illustrated. The C-domain overhanging segment is labelled as
the H2-motif. (b) Electrostatic surface potentials of
CtMfe2p(dh[a+b]D) ligand-binding pocket with the bound
(3R)-hydroxydecanoyl-CoA (Protein Data Bank accession code ID
1PN417). The ligand binds to the positively charged CoA-binding
pocket in a bent conformation, where the adenine ring of the
3'-phosphate-ADP moiety points toward the protein, while the
phosphate groups are solvent-exposed. The stronger positive
charge at the surface of the ligand-binding pocket of
CtMfe2p(dh[a+b]D) is created by the side-chains of two lysine
residues (Lys820 and Lys823 of the C-domain overhanging segment)
and an arginine (Arg760 of b-strand b5), which are not found in
HsMFE-2(dDhSCP-2LD). Nevertheless, those residues are not
directly involved in substrate binding. (c) A close-up view of
the CoA-binding pocket after superimposing the apo form of
HsMFE-2(dDhSCP-2LD) (magenta) with the holo form of
CtMfe2p(dh[a+b]D) (light gray). The salt bridge between the
Lys729 of CtMfe2p(dh[a+b]D) and 3'-phosphate of the substrate as
well as the stacking interaction between Arg855 of
CtMfe2p(dh[a+b]D) and adenine ring of the substrate are shown
with black lines. (d) The differences in the region of the
flexible loop I of hydratase 2s from human (green), C.
tropicalis apoenzyme (gray) and C. tropicalis holoenzyme (red)
after superimposition of the three structures. The
(3R)-hydroxydecanoyl-CoA molecule of the C. tropicalis
holoenzyme is also shown. The b-strands b2 and b5 and the
C-domain are only partially shown for clarity. The side-chains
of Met386 and Val404 of HsMFE-2(dDhSCP-2LD) (in pink) as well as
Leu697 of CtMfe2p(dh[a+b]D) (in yellow) are shown. The black
arrow points to the position of the a-methyl group of
branched-chain fatty acids.
|
