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Figure 2.
The structure of CcmM (A) Structure of the CcmM209 monomer,
with secondary structure labeled. (B) CcmM209 trimer viewed down
the 3-fold axis. The zinc binding histidine residues, as well as
R121 (which binds a structural chloride ion), are shown in
sticks. The zinc ion is shown as a pink sphere. (C) The CcmM209
trimer viewed orthogonal to the 3-fold axis. Individual monomers
are arranged with the β-helical axis parallel to one another,
while αC interacts with the adjacent protomer. (D) Details of
the inset area, with σA weighted 2mF[o]-DF[c] electron density
contoured at 1.0σ (blue) shown for residues E171–L208 of
chain A (orange sticks), and for residues P9– L17 of chain B
(yellow sticks). Electron density in this region is well
defined, with temperature factors comparable to elsewhere in the
structure. Density is also contoured at 3.0σ (green surface)
for C194 and C200, showing the density associated with the
sulfur atoms participating in the disulfide bond. For
comparison, V182 is the last residue ordered in the CcmM193
structure. (E) Superposition of apo zinc Cam (1qrg; white and
yellow) on CcmM209 (blue, αC in orange). Aside from the
highlighted localized differences, the two structures are
overall very similar. (F) Ribbon diagram of CcmM193 (white)
superimposed on CcmM209 (blue) demonstrating that structural
differences are localized, but substantial. Residues 4–16
(orange in CcmM209) are disordered in the CcmM193 structure. Of
residues 172–208, which in CcmM209 comprise αB and αC
(brown), only residues 172–182 are partially ordered in the
CcmM193 structure (red), and these residues are displaced from
the position seen in CcmM209. (G) Inset showing electron density
for the CcmM193 structure. Density is contoured at 1σ (light
blue) and 4σ (dark blue). The electron density for αB is
considerably less defined than for the rest of the structure.
(H) The oligomeric organization differs between CcmM209 (blue)
and CcmM193 (white) structures. The structures were superimposed
with reference to the protomer on the right only. The motion the
CcmM193 and CcmM209 structures can be described as the rotation
of each protomer approximately 6° away from the 3-fold axis,
with the fulcrum located near R121. (I) Details of the CcmM209
catalytic site. The αB helix, which covers the catalytic site,
is shown in cyan in transparent cartoon representation. (J)
Details of the CcmM193 putative catalytic site. Residues labeled
“b” are contributed by a symmetry related molecule. (K)
Superposition of the CcmM209 active site (blue) on CcmM193
(white). Note that many of the residues contributed by the
“b” side of the pocket are misplaced in CcmM193 and fail to
form hydrogen bonds important for catalytic activity. (L)
Overlay of the CcmM209 (blue) and Cam (yellow) catalytic sites.
Note that, despite the low overall sequence identity (∼35%),
all catalytic site residues are conserved and adopt identical
conformations. See Fig. S3 for details of the metal ion
geometry, and Fig. S4 for further details of the catalytic site.
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