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PDBsum entry 3co2

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protein Protein-protein interface(s) links
Membrane protein PDB id
3co2
Jmol
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 21 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q98GN8  (CNGK1_RHILO) -  Cyclic nucleotide-gated potassium channel mll3241
Seq:
Struc:
355 a.a.
126 a.a.*
Protein chain
Pfam   ArchSchema ?
Q98GN8  (CNGK1_RHILO) -  Cyclic nucleotide-gated potassium channel mll3241
Seq:
Struc:
355 a.a.
119 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22230959 T.I.Brelidze, A.E.Carlson, B.Sankaran, and W.N.Zagotta (2012).
Structure of the carboxy-terminal region of a KCNH channel.
  Nature, 481, 530-533.
PDB codes: 3ukn 3ukt 3ukv
20729090 A.Cukkemane, R.Seifert, and U.B.Kaupp (2011).
Cooperative and uncooperative cyclic-nucleotide-gated ion channels.
  Trends Biochem Sci, 36, 55-64.  
21430265 S.Schünke, M.Stoldt, J.Lecher, U.B.Kaupp, and D.Willbold (2011).
Structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from Mesorhizobium loti K1 channel.
  Proc Natl Acad Sci U S A, 108, 6121-6126.
PDB code: 2kxl
19525958 J.W.Taraska, M.C.Puljung, N.B.Olivier, G.E.Flynn, and W.N.Zagotta (2009).
Mapping the structure and conformational movements of proteins with transition metal ion FRET.
  Nat Methods, 6, 532-537.
PDB codes: 3etq 3ffq
19671703 T.I.Brelidze, A.E.Carlson, and W.N.Zagotta (2009).
Absence of direct cyclic nucleotide modulation of mEAG1 and hERG1 channels revealed with fluorescence and electrophysiological methods.
  J Biol Chem, 284, 27989-27997.  
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