PDBsum entry 2ccn

Four helix bundle

PDB id

2ccn

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Contents

			Protein chains

					33 a.a.

			Waters ×83

PDB id:

2ccn

Links

Name:

Four helix bundle

Title:

Pli e20c is antiparallel

Structure:

General control protein gcn4. Chain: a, b. Fragment: residues 249-281. Synonym: amino acid biosynthesis regulatory protein. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.60Å

R-factor:

0.219

R-free:

0.259

Authors:

M.K.Yadav,L.J.Leman,D.J.Price,C.L.Brooks 3rd,C.D.Stout,M.R.Ghadiri

Key ref:

M.K.Yadav et al. (2006). Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry, 45, 4463-4473. PubMed id: 16584182 DOI: 10.1021/bi060092q

Date:

16-Jan-06

Release date:

06-Apr-06

Supersedes:

1vzl

PROCHECK

	Headers

	References

Protein chains

P03069 (GCN4_YEAST) - General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					281 a.a. 33 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

DOI no: 10.1021/bi060092q	Biochemistry 45:4463-4473 (2006)
PubMed id: 16584182

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.
M.K.Yadav, L.J.Leman, D.J.Price, C.L.Brooks, C.D.Stout, M.R.Ghadiri.

ABSTRACT

A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represent the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to the helix register and side-chain conformations that accommodate the two configurations and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21280805

R.I.Cukier (2011).
A Hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.

J Chem Phys, 134, 045104.

20181714

F.Hoh, M.Uzest, M.Drucker, C.Plisson-Chastang, P.Bron, S.Blanc, and C.Dumas (2010).
Structural insights into the molecular mechanisms of cauliflower mosaic virus transmission by its insect vector.

J Virol, 84, 4706-4713.

PDB codes:

3f6n 3k4t

19805278

D.Albanesi, M.Martín, F.Trajtenberg, M.C.Mansilla, A.Haouz, P.M.Alzari, D.de Mendoza, and A.Buschiazzo (2009).
Structural plasticity and catalysis regulation of a thermosensor histidine kinase.

Proc Natl Acad Sci U S A, 106, 16185-16190.

PDB codes:

3ehf 3ehh 3ehj 3gie 3gif 3gig

19580264

M.W.Giuliano, W.S.Horne, and S.H.Gellman (2009).
An alpha/beta-peptide helix bundle with a pure beta3-amino acid core and a distinctive quaternary structure.

J Am Chem Soc, 131, 9860-9861.

PDB codes:

3f86 3f87

19693805

Q.Xu, and D.L.Minor (2009).
Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif.

Protein Sci, 18, 2100-2114.

PDB codes:

3hfc 3hfe

18704948

S.S.Pendley, Y.B.Yu, and T.E.Cheatham (2009).
Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.

Proteins, 74, 612-629.

19506258

Y.Gambin, A.Schug, E.A.Lemke, J.J.Lavinder, A.C.Ferreon, T.J.Magliery, J.N.Onuchic, and A.A.Deniz (2009).
Direct single-molecule observation of a protein living in two opposed native structures.

Proc Natl Acad Sci U S A, 106, 10153-10158.

18791833

G.Fernández-Ballester, and A.Ferrer-Montiel (2008).
Molecular modeling of the full-length human TRPV1 channel in closed and desensitized states.

J Membr Biol, 223, 161-172.

18555680

G.Grigoryan, and A.E.Keating (2008).
Structural specificity in coiled-coil interactions.

Curr Opin Struct Biol, 18, 477-483.

18782578

Y.Fujiwara, and D.L.Minor (2008).
X-ray crystal structure of a TRPM assembly domain reveals an antiparallel four-stranded coiled-coil.

J Mol Biol, 383, 854-870.

PDB code:

3e7k

17609383

D.S.Touw, C.E.Nordman, J.A.Stuckey, and V.L.Pecoraro (2007).
Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils.

Proc Natl Acad Sci U S A, 104, 11969-11974.

PDB code:

2jgo

17302417

L.J.Leman, D.A.Weinberger, Z.Z.Huang, K.M.Wilcoxen, and M.R.Ghadiri (2007).
Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering.

J Am Chem Soc, 129, 2959-2966.

17189475

Y.Deng, Q.Zheng, J.Liu, C.S.Cheng, N.R.Kallenbach, and M.Lu (2007).
Self-assembly of coiled-coil tetramers in the 1.40 A structure of a leucine-zipper mutant.

Protein Sci, 16, 323-328.

PDB code:

2nrn

17030805

J.Liu, Q.Zheng, Y.Deng, C.S.Cheng, N.R.Kallenbach, and M.Lu (2006).
A seven-helix coiled coil.

Proc Natl Acad Sci U S A, 103, 15457-15462.

PDB code:

2hy6

16959572

M.Hulko, F.Berndt, M.Gruber, J.U.Linder, V.Truffault, A.Schultz, J.Martin, J.E.Schultz, A.N.Lupas, and M.Coles (2006).
The HAMP domain structure implies helix rotation in transmembrane signaling.

Cell, 126, 929-940.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.