 |
PDBsum entry 3co2
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Membrane protein
|
PDB id
|
|
|
|
3co2
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structural and energetic analysis of activation by a cyclic nucleotide binding domain.
|
|
|
Authors
|
|
S.L.Altieri,
G.M.Clayton,
W.R.Silverman,
A.O.Olivares,
E.M.De la cruz,
L.R.Thomas,
J.H.Morais-Cabral.
|
|
|
Ref.
|
|
J Mol Biol, 2008,
381,
655-669.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
MlotiK1 is a prokaryotic homolog of cyclic-nucleotide-dependent ion channels
that contains an intracellular C-terminal cyclic nucleotide binding (CNB)
domain. X-ray structures of the CNB domain have been solved in the absence of
ligand and bound to cAMP. Both the full-length channel and CNB domain fragment
are easily expressed and purified, making MlotiK1 a useful model system for
dissecting activation by ligand binding. We have used X-ray crystallography to
determine three new MlotiK1 CNB domain structures: a second apo configuration, a
cGMP-bound structure, and a second cAMP-bound structure. In combination, the
five MlotiK1 CNB domain structures provide a unique opportunity for analyzing,
within a single protein, the structural differences between the apo state and
the bound state, and the structural variability within each state. With this
analysis as a guide, we have probed the nucleotide selectivity and importance of
specific residue side chains in ligand binding and channel activation. These
data help to identify ligand-protein interactions that are important for ligand
dependence in MlotiK1 and, more globally, in the class of nucleotide-dependent
proteins.
|
|
|
|
|
|
|
|
Figure 8.
Fig. 8. C- and B-helix features in the bound and apo states.
(a) Three different αC-helix arrangements: cAMP-bound wild-type
(red), partially unwound (R348A in gray) and disordered (R307W
in green). The circle indicates the position of Phe341, a
residue referred to in the text (the R307W structure lacks this
residue). (b) Three examples of the αB-helix arrangement
emphasizing how it occupies two orientations: bound (wild-type
in red) and apo (R348A in gray and R307W in green). The circle
indicates the position of Leu330 (see the text).
|
|
Figure 9.
Fig. 9. Features of the binding pocket. (a) Overlay of the
binding pockets (residues 295–312) of two bound [wild-type
cAMP (red) and R307E (red)] and five [apo: R348A (gray) and
R307W (green)] structures. Glu298 and Met299, both highly
mobile, are highlighted. The side chains of Leu301 and position
307 (various mutants), as well as cAMP, are shown for reference.
(b) The positions of Leu301 and Phe327 in the bound (tan) and
apo (green) structures showing clear differences in the position
of the side chains between the two states, but not among the
structures in the individual states. (c) The position of the
Arg307 side chain is invariant regardless of state or mutation.
Side-chain position shown: R307 from cAMP-bound wild type (red),
R307 from the R348A apo structure (gray), Glu307 from the
R307E-bound structure (cyan), and two different Trp307 from the
R307W apo structure (green). (d) Stabilization of position 307
by interactions between its main chain and residues of a
parallel loop. Hydrogen bonds between the backbones at Arg307,
Gly266, and Glu267 from the cAMP-bound wild-type structure are
shown.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2008,
381,
655-669)
copyright 2008.
|
|
|
|
|
|
|
