PDBsum entry 1uo2

Four helix bundle

PDB id

1uo2

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Contents

			Protein chains

					33 a.a.

			Waters ×30

PDB id:

1uo2

Links

Name:

Four helix bundle

Title:

Structure based engineering of internal molecular surfaces of four helix bundles

Structure:

General control protein gcn4. Chain: a, b. Synonym: gcn4 leucine zipper, amino acid biosynthesis regulatory protein, pl1. Engineered: yes. Other_details: dimer asymmetric unit of four helix bundle

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Other_details: based on sequence from saccharomyces cerevisiae (baker's yeast)

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.99Å

R-factor:

0.242

R-free:

0.286

Authors:

M.K.Yadav,J.E.Redman,J.M.Alvarez-Gutierrez,Y.Zhang,C.D.Stout, M.R.Ghadiri

Key ref:

M.K.Yadav et al. (2005). Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry, 44, 9723-9732. PubMed id: 16008357 DOI: 10.1021/bi050742a

Date:

15-Sep-03

Release date:

13-Oct-04

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 8 residue positions (black crosses)

DOI no: 10.1021/bi050742a	Biochemistry 44:9723-9732 (2005)
PubMed id: 16008357

Structure-based engineering of internal cavities in coiled-coil peptides.
M.K.Yadav, J.E.Redman, L.J.Leman, J.M.Alvarez-Gutiérrez, Y.Zhang, C.D.Stout, M.R.Ghadiri.

ABSTRACT

Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20564030

W.Nomura, T.Mino, T.Narumi, N.Ohashi, A.Masuda, C.Hashimoto, H.Tsutsumi, and H.Tamamura (2010).
Development of crosslink-type tag-probe pairs for fluorescent imaging of proteins.

Biopolymers, 94, 843-852.

19579245

A.F.Peacock, J.A.Stuckey, and V.L.Pecoraro (2009).
Switching the chirality of the metal environment alters the coordination mode in designed peptides.

Angew Chem Int Ed Engl, 48, 7371-7374.

PDB codes:

3h5f 3h5g

19241380

A.S.Olia, S.Casjens, and G.Cingolani (2009).
Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.

Protein Sci, 18, 537-548.

PDB code:

3c9i

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.

18213666

Z.Z.Huang, L.J.Leman, and M.R.Ghadiri (2008).
Biomimetic catalysis of diketopiperazine and dipeptide syntheses.

Angew Chem Int Ed Engl, 47, 1758-1761.

17243796

K.M.Wilcoxen, L.J.Leman, D.A.Weinberger, Z.Z.Huang, and M.R.Ghadiri (2007).
Biomimetic catalysis of intermodular aminoacyl transfer.

J Am Chem Soc, 129, 748-749.

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.

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.

16584182

M.K.Yadav, L.J.Leman, D.J.Price, C.L.Brooks, C.D.Stout, and M.R.Ghadiri (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.

PDB codes:

1w5h 1w5j 1w5k 1w5l 2cce 2ccf 2ccn

16257571

W.J.Cooper, and M.L.Waters (2005).
Molecular recognition with designed peptides and proteins.

Curr Opin Chem Biol, 9, 627-631.

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.