PDBsum entry 1ce9

Helix capping

PDB id: 1ce9

Contents

Protein chains

34 a.a.

Waters ×150

PDB id:

1ce9

Name:

Helix capping

Title:

Helix capping in the gcn4 leucine zipper

Structure:

Protein (gcn4-pmse). Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Synthetic: yes

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.214 R-free: 0.283

Authors:

M.Lu,W.Shu,H.Ji,E.Spek,L.-Y.Wang,N.R.Kallenbach

Key ref:

M.Lu et al. (1999). Helix capping in the GCN4 leucine zipper. J Mol Biol, 288, 743-752. PubMed id: 10329176 DOI: 10.1006/jmbi.1999.2707

Date:

18-Mar-99 Release date: 25-Mar-99

Protein chains

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

Seq: 281 a.a.

Struc: 34 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DOI no: 10.1006/jmbi.1999.2707

J Mol Biol 288:743-752 (1999)

PubMed id: 10329176

Helix capping in the GCN4 leucine zipper.

M.Lu, W.Shu, H.Ji, E.Spek, L.Wang, N.R.Kallenbach.

ABSTRACT

Capping interactions associated with specific sequences at or near the ends of alpha-helices are important determinants of the stability of protein secondary and tertiary structure. We investigate here the role of the helix-capping motif Ser-X-X-Glu, a sequence that occurs frequently at the N termini of alpha helices in proteins, on the conformation and stability of the GCN4 leucine zipper. The 1.8 A resolution crystal structure of the capped molecule reveals distinct conformations, packing geometries and hydrogen-bonding networks at the amino terminus of the two helices in the leucine zipper dimer. The free energy of helix stabilization associated with the hydrogen-bonding and hydrophobic interactions in this capping structure is -1.2 kcal/mol, evaluated from thermal unfolding experiments. A single cap thus contributes appreciably to stabilizing the terminated helix and thereby the native state. These results suggest that helix capping plays a further role in protein folding, providing a sensitive connector linking alpha-helix formation to the developing tertiary structure of a protein.

Selected figure(s)

Figure 2.
Figure 2. Folding of the GCN4 leucine zipper mutant peptides as a-helical dimers. (a) CD spectra of GCN4- pMSE (open circles), GCN4-pSE (open squares), and GCN4-pAA (open triangles) at 0 ° C in PBS (pH 7.0) and 10 mM peptide. (b) Temperature-dependence of the CD signal at 222 nm for GCN4-pMSE (open circles), GCN4- pSE (open squares), and GCN4-pAA (open triangles) in PBS (pH 7.0) and 10 mM peptide. (c) Representative sedimentation equilibrium data (35 krpm) for GCN4- pMSE collected at 20 °C and ~300 mM peptide. The ran- dom distribution of the residuals indicates that the data fit well to an ideal single-species model.

Figure 3.
Figure 3. Stereo view of the crystal structure of the GCN4-pMSE dimer. An axial view of the two a-helical coiled-coil dimers of the unit cell. Water molecules are indicated with blue dots. The view is from the amino terminus down the superhelix axis of the coiled-coil dimer, colored yellow, and the carboxyl terminus of the coiled-coil dimer, colored green. The Figure was pre- pared using the program SETOR (Evans, 1993).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 743-752) copyright 1999.

Figures were selected by an automated process.