PDBsum entry 3co2

Membrane protein

PDB id: 3co2

Contents

Protein chains

126 a.a. *

119 a.a. *

Waters ×9

* Residue conservation analysis

PDB id:

3co2

Name:

Membrane protein

Title:

Mlotik1 ion channel cyclic-nucleotide binding domain mutant

Structure:

Mlotik1 ion channel protein. Chain: a, b, c, d. Fragment: cyclic-nucleotide binding domain (unp residues 216-355). Engineered: yes. Mutation: yes

Source:

Mesorhizobium loti. Expressed in: escherichia coli.

Resolution:

2.90Å R-factor: 0.263 R-free: 0.306

Authors:

G.M.Clayton,S.L.Alteiri,L.R.Thomas,J.H.Morais-Cabral

Key ref:

S.L.Altieri et al. (2008). Structural and energetic analysis of activation by a cyclic nucleotide binding domain. J Mol Biol, 381, 655-669. PubMed id: 18619611 DOI: 10.1016/j.jmb.2008.06.011

Date:

27-Mar-08 Release date: 05-Aug-08

Protein chains

Q98GN8  (CNGK1_RHILO) -  Cyclic nucleotide-gated potassium channel mll3241 from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)

Seq: 355 a.a.

Struc: 126 a.a.*

Protein chain

Q98GN8  (CNGK1_RHILO) -  Cyclic nucleotide-gated potassium channel mll3241 from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)

Seq: 355 a.a.

Struc: 119 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2008.06.011

J Mol Biol 381:655-669 (2008)

PubMed id: 18619611

Structural and energetic analysis of activation by a cyclic nucleotide binding domain.

S.L.Altieri, G.M.Clayton, W.R.Silverman, A.O.Olivares, E.M.De la Cruz, L.R.Thomas, J.H.Morais-Cabral.

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.

Selected figure(s)

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.

Figures were selected by an automated process.