2R2V

Sequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil

Summary for 2R2V

• Entry DOI: 10.2210/pdb2r2v/pdb
• Related: 2ZTA
• Descriptor: GCN4 leucine zipper, ZINC ION, ACETATE ION, ... (5 entities in total)
• Functional Keywords: coiled coils, anti-parallel tetramer, protein design, de novo protein
• Biological source: SACCHAROMYCES CEREVISIAE (YEAST)
• Total number of polymer chains: 8
• Total formula weight: 32072.87

Authors

Liu, J.,Lu, M. (deposition date: 2007-08-27, release date: 2008-06-17, Last modification date: 2023-08-30)

Primary citation

Liu, J.,Zheng, Q.,Deng, Y.,Li, Q.,Kallenbach, N.R.,Lu, M.
Conformational specificity of the lac repressor coiled-coil tetramerization domain.
Biochemistry, 46:14951-14959, 2007

PubMed Abstract: Predictive understanding of how the folded, functional shape of a native protein is encoded in the linear sequence of its amino acid residues remains an unsolved challenge in modern structural biology. Antiparallel four-stranded coiled coils are relatively simple protein structures that embody a heptad sequence repeat and rich diversity for tertiary packing of alpha-helices. To explore specific sequence determinants of the lac repressor coiled-coil tetramerization domain, we have engineered a set of buried nonpolar side chains at the a-, d-, and e-positions into the hydrophobic interior of the dimeric GCN4 leucine zipper. Circular dichroism and equilibrium ultracentrifugation studies show that this core variant (GCN4-pAeLV) forms a stable tetrameric structure with a reversible and highly cooperative thermal unfolding transition. The X-ray crystal structure at 1.9 A reveals that GCN4-pAeLV is an antiparallel four-stranded coiled coil of the lac repressor type in which the a, d, and e side chains associate by means of combined knobs-against-knobs and knobs-into-holes packing with a characteristic interhelical offset of 0.25 heptad. Comparison of the side chain shape and packing in the antiparallel tetramers shows that the burial of alanine residues at the e positions between the neighboring helices of GCN4-pAeLV dictates both the antiparallel orientation and helix offset. This study fills in a gap in our knowledge of the determinants of structural specificity in antiparallel coiled coils and improves our understanding of how specific side chain packing forms the teritiary structure of a functional protein.

PubMed: 18052214
DOI: 10.1021/bi701930d

Experimental method

X-RAY DIFFRACTION (1.9 Å)