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| | ==Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles== | | ==Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles== |
| - | <StructureSection load='1unu' size='340' side='right' caption='[[1unu]], [[Resolution|resolution]] 2.07Å' scene=''> | + | <StructureSection load='1unu' size='340' side='right'caption='[[1unu]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1unu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UNU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UNU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1unu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UNU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.07Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gcl|1gcl]], [[1gcm|1gcm]], [[1unt|1unt]], [[1unv|1unv]], [[1unw|1unw]], [[1unx|1unx]], [[1uny|1uny]], [[1unz|1unz]], [[1uo0|1uo0]], [[1uo1|1uo1]], [[1uo2|1uo2]], [[1uo3|1uo3]], [[1uo4|1uo4]], [[1uo5|1uo5]]</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=1unu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1unu OCA], [https://pdbe.org/1unu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1unu RCSB], [https://www.ebi.ac.uk/pdbsum/1unu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1unu 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=1unu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1unu OCA], [http://pdbe.org/1unu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1unu RCSB], [http://www.ebi.ac.uk/pdbsum/1unu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1unu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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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| | ==See Also== | | ==See Also== |
| - | *[[Gcn4|Gcn4]] | + | *[[Gcn4 3D Structures|Gcn4 3D Structures]] |
| | + | *[[Gnc4 3D Structures|Gnc4 3D Structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Alvarez-Gutierrez, J M]] | + | [[Category: Large Structures]] |
| - | [[Category: Ghadiri, M R]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Redman, J E]] | + | [[Category: Alvarez-Gutierrez JM]] |
| - | [[Category: Stout, C D]] | + | [[Category: Ghadiri MR]] |
| - | [[Category: Yadav, M K]] | + | [[Category: Redman JE]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Stout CD]] |
| - | [[Category: Cavity]] | + | [[Category: Yadav MK]] |
| - | [[Category: Four helix bundle]] | + | [[Category: Zhang Y]] |
| Structural highlights
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
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.
Structure-based engineering of internal cavities in coiled-coil peptides.,Yadav MK, Redman JE, Leman LJ, Alvarez-Gutierrez JM, Zhang Y, Stout CD, Ghadiri MR Biochemistry. 2005 Jul 19;44(28):9723-32. PMID:16008357[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yadav MK, Redman JE, Leman LJ, Alvarez-Gutierrez JM, Zhang Y, Stout CD, Ghadiri MR. Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry. 2005 Jul 19;44(28):9723-32. PMID:16008357 doi:10.1021/bi050742a
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