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PDBsum entry 1swi
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protein ligands Protein-protein interface(s) links
Leucine zipper PDB id
1swi

 

 

 

 

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Contents
Protein chains
31 a.a.
30 a.a.
Ligands
BNZ
Waters ×29
PDB id:
1swi
Name: Leucine zipper
Title: Gcn4-leucine zipper core mutant as n16a complexed with benzene
Structure: Gcn4p1. Chain: a, b, c. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Trimer (from PQS)
Resolution:
2.60Å     R-factor:   0.187    
Authors: L.Gonzalez,J.Plecs,T.Alber
Key ref: L.Gonzalez et al. (1996). An engineered allosteric switch in leucine-zipper oligomerization. Nat Struct Biol, 3, 510-515. PubMed id: 8646536
Date:
09-May-96     Release date:   08-Nov-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		281 a.a.
31 a.a.*
Protein chains
Pfam   ArchSchema ?
P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		281 a.a.
30 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Nat Struct Biol 3:510-515 (1996)
PubMed id: 8646536  
 
 
An engineered allosteric switch in leucine-zipper oligomerization.
L.Gonzalez, J.J.Plecs, T.Alber.
 
  ABSTRACT  
 
Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide-benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20676430 B.Apostolovic, M.Danial, and H.A.Klok (2010).
Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials.
  Chem Soc Rev, 39, 3541-3575.  
19598226 D.Shiga, D.Nakane, T.Inomata, H.Masuda, M.Oda, M.Noda, S.Uchiyama, K.Fukui, Y.Takano, H.Nakamura, T.Mizuno, and T.Tanaka (2009).
The effect of the side chain length of Asp and Glu on coordination structure of Cu(2+) in a de novo designed protein.
  Biopolymers, 91, 907-916.  
19241406 L.Röglin, F.Altenbrunn, and O.Seitz (2009).
DNA and RNA-controlled switching of protein kinase activity.
  Chembiochem, 10, 758-765.  
19099065 L.Roy, and M.A.Case (2009).
Electrostatic determinants of stability in parallel 3-stranded coiled coils.
  Chem Commun (Camb), (), 192-194.  
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.  
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
16008357 M.K.Yadav, J.E.Redman, L.J.Leman, J.M.Alvarez-Gutiérrez, Y.Zhang, C.D.Stout, and M.R.Ghadiri (2005).
Structure-based engineering of internal cavities in coiled-coil peptides.
  Biochemistry, 44, 9723-9732.
PDB codes: 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5i 2bni
16257571 W.J.Cooper, and M.L.Waters (2005).
Molecular recognition with designed peptides and proteins.
  Curr Opin Chem Biol, 9, 627-631.  
14752198 J.Holton, and T.Alber (2004).
Automated protein crystal structure determination using ELVES.
  Proc Natl Acad Sci U S A, 101, 1537-1542.
PDB codes: 1rb1 1rb4 1rb5 1rb6 3k7z
14760737 J.M.Mason, and K.M.Arndt (2004).
Coiled coil domains: stability, specificity, and biological implications.
  Chembiochem, 5, 170-176.  
15020585 S.C.Kwok, and R.S.Hodges (2004).
Stabilizing and destabilizing clusters in the hydrophobic core of long two-stranded alpha-helical coiled-coils.
  J Biol Chem, 279, 21576-21588.  
15345544 T.Stockner, W.L.Ash, J.L.MacCallum, and D.P.Tieleman (2004).
Direct simulation of transmembrane helix association: role of asparagines.
  Biophys J, 87, 1650-1656.  
12649422 W.F.DeGrado, H.Gratkowski, and J.D.Lear (2003).
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles.
  Protein Sci, 12, 647-665.  
12202385 H.Gratkowski, Q.H.Dai, A.J.Wand, W.F.DeGrado, and J.D.Lear (2002).
Cooperativity and specificity of association of a designed transmembrane peptide.
  Biophys J, 83, 1613-1619.  
12138097 J.R.Litowski, and R.S.Hodges (2002).
Designing heterodimeric two-stranded alpha-helical coiled-coils. Effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity.
  J Biol Chem, 277, 37272-37279.  
12163069 T.O.Yeates, and J.E.Padilla (2002).
Designing supramolecular protein assemblies.
  Curr Opin Struct Biol, 12, 464-470.  
12384310 Y.B.Yu (2002).
Coiled-coils: stability, specificity, and drug delivery potential.
  Adv Drug Deliv Rev, 54, 1113-1129.  
11373720 I.Obataya, S.Sakamoto, A.Ueno, and H.Mihara (2001).
Design and synthesis of 3alpha-helix peptides forming a cavity for a fluorescent ligand.
  Biopolymers, 59, 65-71.  
11714921 K.Dutta, A.Alexandrov, H.Huang, and S.M.Pascal (2001).
pH-induced folding of an apoptotic coiled coil.
  Protein Sci, 10, 2531-2540.  
  11206050 P.Burkhard, M.Meier, and A.Lustig (2000).
Design of a minimal protein oligomerization domain by a structural approach.
  Protein Sci, 9, 2294-2301.
PDB code: 1hqj
10716989 P.R.Mittl, C.Deillon, D.Sargent, N.Liu, S.Klauser, R.M.Thomas, B.Gutte, and M.G.Grütter (2000).
The retro-GCN4 leucine zipper sequence forms a stable three-dimensional structure.
  Proc Natl Acad Sci U S A, 97, 2562-2566.
PDB code: 1c94
11241216 T.Kiyokawa, K.Kanaori, K.Tajima, and T.Tanaka (2000).
Engineering of the hydrophobic core of an alpha-helical coiled coil.
  Biopolymers, 55, 407-414.  
10856217 Z.Guo, D.Zhou, and P.G.Schultz (2000).
Designing small-molecule switches for protein-protein interactions.
  Science, 288, 2042-2045.  
  10631975 G.A.Lazar, E.C.Johnson, J.R.Desjarlais, and T.M.Handel (1999).
Rotamer strain as a determinant of protein structural specificity.
  Protein Sci, 8, 2598-2610.
PDB code: 1c3t
9915333 J.S.Johansson, H.Zou, and J.W.Tanner (1999).
Bound volatile general anesthetics alter both local protein dynamics and global protein stability.
  Anesthesiology, 90, 235-245.  
10368295 K.Håkansson, N.K.Lim, H.J.Hoppe, and K.B.Reid (1999).
Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D.
  Structure, 7, 255-264.
PDB code: 1b08
  10595534 K.Wagschal, B.Tripet, P.Lavigne, C.Mant, and R.S.Hodges (1999).
The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.
  Protein Sci, 8, 2312-2329.  
10318791 M.J.Arrizubieta, and E.Bandman (1999).
Regulation of alpha-helical coiled-coil dimerization in chicken skeletal muscle light meromyosin.
  J Biol Chem, 274, 13847-13853.  
10872466 W.F.DeGrado, C.M.Summa, V.Pavone, F.Nastri, and A.Lombardi (1999).
De novo design and structural characterization of proteins and metalloproteins.
  Annu Rev Biochem, 68, 779-819.  
  10422826 Z.S.Hendsch, and B.Tidor (1999).
Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding.
  Protein Sci, 8, 1381-1392.  
10226028 Z.Zhang, A.Murphy, J.C.Hu, and T.Kodadek (1999).
Genetic selection of short peptides that support protein oligomerization in vivo.
  Curr Biol, 9, 417-420.  
9914192 G.A.Lazar, and T.M.Handel (1998).
Hydrophobic core packing and protein design.
  Curr Opin Chem Biol, 2, 675-679.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
9736606 Y.Guo, D.Bozic, V.N.Malashkevich, R.A.Kammerer, T.Schulthess, and J.Engel (1998).
All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.
  EMBO J, 17, 5265-5272.
PDB code: 1fbm
9667893 B.R.Gibney, F.Rabanal, and P.L.Dutton (1997).
Synthesis of novel proteins.
  Curr Opin Chem Biol, 1, 537-542.  
  9194187 L.Szilák, J.Moitra, and C.Vinson (1997).
Design of a leucine zipper coiled coil stabilized 1.4 kcal mol-1 by phosphorylation of a serine in the e position.
  Protein Sci, 6, 1273-1283.  
8946853 L.Gonzalez, R.A.Brown, D.Richardson, and T.Alber (1996).
Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.
  Nat Struct Biol, 3, 1002-1009.
PDB codes: 1zii 1zij
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.

 

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