|
|
| Line 1: |
Line 1: |
| | | | |
| | ==NMR Structures Show Unwinding of the GCN4p Coiled Coil Superhelix Accompanying Disruption of Ion Pairs at Acidic pH== | | ==NMR Structures Show Unwinding of the GCN4p Coiled Coil Superhelix Accompanying Disruption of Ion Pairs at Acidic pH== |
| - | <StructureSection load='5iir' size='340' side='right'caption='[[5iir]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='5iir' size='340' side='right'caption='[[5iir]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5iir]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IIR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IIR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5iir]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IIR FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iiv|5iiv]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GCN4, AAS3, ARG9, YEL009C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=5iir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iir OCA], [https://pdbe.org/5iir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iir RCSB], [https://www.ebi.ac.uk/pdbsum/5iir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iir ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5iir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iir OCA], [http://pdbe.org/5iir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iir RCSB], [http://www.ebi.ac.uk/pdbsum/5iir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iir 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 == |
| Line 21: |
Line 20: |
| | | | |
| | ==See Also== | | ==See Also== |
| | + | *[[Gcn4 3D Structures|Gcn4 3D Structures]] |
| | *[[Gnc4 3D Structures|Gnc4 3D Structures]] | | *[[Gnc4 3D Structures|Gnc4 3D Structures]] |
| | == References == | | == References == |
| Line 26: |
Line 26: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Alexandrescu, A T]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Brady, M R]] | + | [[Category: Alexandrescu AT]] |
| - | [[Category: Kaplan, A R]] | + | [[Category: Brady MR]] |
| - | [[Category: Canonical alpha helix]] | + | [[Category: Kaplan AR]] |
| - | [[Category: Closely related nmr structure]]
| + | |
| - | [[Category: Conformational transition]]
| + | |
| - | [[Category: Electrostatic]]
| + | |
| - | [[Category: Knobs-into-hole]]
| + | |
| - | [[Category: Leucine zipper]]
| + | |
| - | [[Category: Salt bridge]]
| + | |
| - | [[Category: Supercoil parameter]]
| + | |
| - | [[Category: Transcription]]
| + | |
| 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
To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The alpha-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Calpha, and Cbeta) of GCN4p display a seven-residue periodicity that is consistent with alpha-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1H-15N nuclear Overhauser effect relaxation measurements, the alpha-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13C rotating frame T1 relaxation (T1rho) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.
Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.,Kaplan AR, Brady MR, Maciejewski MW, Kammerer RA, Alexandrescu AT Biochemistry. 2017 Mar 9. doi: 10.1021/acs.biochem.6b00634. PMID:28230348[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kaplan AR, Brady MR, Maciejewski MW, Kammerer RA, Alexandrescu AT. Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix. Biochemistry. 2017 Mar 9. doi: 10.1021/acs.biochem.6b00634. PMID:28230348 doi:http://dx.doi.org/10.1021/acs.biochem.6b00634
|
