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| | ==Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product== | | ==Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product== |
| - | <StructureSection load='4hu6' size='340' side='right' caption='[[4hu6]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='4hu6' size='340' side='right'caption='[[4hu6]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hu6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HU6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HU6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hu6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HU6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=19W:5-(AMINOOXY)-L-NORVALINE'>19W</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=UU5:(2S)-2-AMINO-4-[(OXOACETYL)AMINO]BUTANOIC+ACID'>UU5</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=19W:5-(AMINOOXY)-L-NORVALINE'>19W</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=UU5:(2S)-2-AMINO-4-[(OXOACETYL)AMINO]BUTANOIC+ACID'>UU5</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hu5|4hu5]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4hu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hu6 OCA], [https://pdbe.org/4hu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hu6 RCSB], [https://www.ebi.ac.uk/pdbsum/4hu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hu6 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4hu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hu6 OCA], [http://pdbe.org/4hu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hu6 RCSB], [http://www.ebi.ac.uk/pdbsum/4hu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hu6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GCN4_YEAST GCN4_YEAST]] Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'. | + | [https://www.uniprot.org/uniprot/GCN4_YEAST GCN4_YEAST] Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4hu6" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4hu6" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Gcn4 3D Structures|Gcn4 3D Structures]] |
| | + | *[[Gnc4 3D Structures|Gnc4 3D Structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Haney, C M]] | + | [[Category: Large Structures]] |
| - | [[Category: Horne, W S]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Side-chain cross-link]] | + | [[Category: Haney CM]] |
| - | [[Category: Side-chain staple]] | + | [[Category: Horne WS]] |
| - | [[Category: Transcription]]
| + | |
| Structural highlights
4hu6 is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
GCN4_YEAST Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'.
Publication Abstract from PubMed
Covalent side-chain cross-links are a versatile method to control peptide folding, particularly when alpha-helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein-protein complex. A series of sequence variants of the dimeric coiled coil GCN4-p1 bearing oxime bridges at solvent-exposed positions were prepared and biophysically characterized. Triggered unmasking of a side-chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X-ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an alpha-helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.
Oxime Side-Chain Cross-Links in an alpha-Helical Coiled-Coil Protein: Structure, Thermodynamics, and Folding-Templated Synthesis of Bicyclic Species.,Haney CM, Horne WS Chemistry. 2013 Aug 19;19(34):11342-51. doi: 10.1002/chem.201300506. Epub 2013, Jul 10. PMID:23843311[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Haney CM, Horne WS. Oxime Side-Chain Cross-Links in an alpha-Helical Coiled-Coil Protein: Structure, Thermodynamics, and Folding-Templated Synthesis of Bicyclic Species. Chemistry. 2013 Aug 19;19(34):11342-51. doi: 10.1002/chem.201300506. Epub 2013, Jul 10. PMID:23843311 doi:10.1002/chem.201300506
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