User:Ann Taylor/Sandbox 1

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==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.
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DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref>
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===Evaluating scenes representing the same structure===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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This sandbox compiles several student-generated scenes that illustrate properties of the Gal4 repressor.
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<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div>
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==Dimer==
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The protein binds as a <scene name='92/925551/Dimer_practice/1'>dimer</scene> to a symmetrical 17-base-pair sequence.
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The protein binds as a <scene name='92/925552/Dimer/1'>dimer</scene> to a symmetrical 17-base-pair sequence.
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<scene name='92/925553/Dimer/1'>Dimer</scene>
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The protein binds as a <scene name='92/925538/Dimer/2'>dimer</scene> to a symmetrical 17-base-pair sequence.
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<scene name='92/927197/Dimer/2'>Dimer</scene>
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==Domains==
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There is a compact <scene name='92/925538/Metal_binding_domain/5'>metal binding domain</scene> (residues 8-40), an <scene name='92/925538/Extended_linker/4'>extended linker</scene> (41-49), and an <scene name='92/925538/Alpha-helical_dimerization/2'>alpha-helical dimerization element</scene> (50-64).
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<scene name='92/925553/Alpha-helical_dimerization_ele/2'>Extended Linker</scene>, <scene name='92/925553/Zinc_binding_domain/1'>Zinc Binding Domain </scene>: Zinc is responsible for maintaining the secondary structure. <scene name='92/925553/Alpha-helical_dimerization_ele/4'>Alpha-Helical Dimerization Element</scene>
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Each subunit folds into three distinct modules: a compact, <scene name='92/925551/Dimer_practice/12'>Metal Binding Domain</scene> (residues 8-40), an <scene name='92/925551/Dimer_practice/4'>Extended Linker</scene> (41-49), and an alpha-helical <scene name='92/925551/Dimer_practice/7'>Dimerization Element</scene> (50-64).
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Each subunit fold into three distinct modules: a compact, <scene name='92/925552/Metal_binding_domain/1'>metal binding domain</scene> (residues 8-40), an <scene name='92/925552/Extended_linker/1'>extended linker</scene> (41-49), and an <scene name='92/925552/Alpha-helical_dimerization/1'>alpha-helical dimerization</scene> element (50-64).
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<scene name='92/927197/Dimer/3'>Text To Be Displayed</scene>
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==Metal binding==
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A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. The metal binding domain contains <scene name='92/925538/Cysteine_metal_binding/3'>cysteine residues</scene> that coordinate to the metal as shown as cadmium.
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The cadmium is coordinated to this domain via interactions with several <scene name='92/925552/Cysteine_coordination_sites/1'>cysteine residues</scene>.
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<scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>
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The Metal Binding Domain binds the metal through the use of <scene name='92/925551/Dimer_practice/13'>cysteine residues</scene>.
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<scene name='92/925553/Dimer_metal_binding_domain/3'>Dimer Metal Binding Domain</scene>
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==DNA/protein interaction==
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The Upstream activation sequence (<scene name='92/925553/Uas/1'>UAS</scene>) for Gal 4.
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Gal4 also contains an upstream activating sequence (<scene name='92/925552/Uas/1'>UAS</scene>) adjacent to that of the promoter region. This sequence works much like an enhancer regions that are common in Eukaryotic genes.
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<scene name='92/925538/Dna_protein_interaction/3'>The DNA-Protein Interaction</scene> with all of the base pairs within 5 angstroms of the protein highlighted illustrates that the protein interacts with both strands of the UAS.
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==See Also==
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*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]
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*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
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== References ==
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<references/>
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__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 18824]]
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[[Category: Large Structures]]
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[[Category: Carey, M]]
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[[Category: Harrison, S C]]
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[[Category: Marmorstein, R]]
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[[Category: Ptashne, M]]
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[[Category: Double helix]]
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[[Category: Protein-dna complex]]
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[[Category: Transcription-dna complex]]

Current revision

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

PDB ID 1d66

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Proteopedia Page Contributors and Editors (what is this?)

Ann Taylor

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