User:Ann Taylor/Sandbox 1: Difference between revisions

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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=''>
== Structural highlights ==
<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>
</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>
<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>
</table>
== Function ==
[[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.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


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>


===Evaluating scenes representing the same structure===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
This sandbox compiles several student-generated scenes that illustrate properties of the Gal4 repressor.
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div>
 
==Dimer==
The protein binds as a <scene name='92/925551/Dimer_practice/1'>dimer</scene> to a symmetrical 17-base-pair sequence.
 
The protein binds as a <scene name='92/925552/Dimer/1'>dimer</scene> to a symmetrical 17-base-pair sequence.
 
<scene name='92/925553/Dimer/1'>Dimer</scene>
 
The protein binds as a <scene name='92/925538/Dimer/2'>dimer</scene> to a symmetrical 17-base-pair sequence.
 
<scene name='92/927197/Dimer/2'>Dimer</scene>
 
==Domains==
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).
 
<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>
 
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).
 
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).
 
<scene name='92/927197/Dimer/3'>Text To Be Displayed</scene>
 
 
==Metal binding==
 
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.
 
The cadmium is coordinated to this domain via interactions with several <scene name='92/925552/Cysteine_coordination_sites/1'>cysteine residues</scene>.
 
<scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>
 
The Metal Binding Domain binds the metal through the use of <scene name='92/925551/Dimer_practice/13'>cysteine residues</scene>.  
 
<scene name='92/925553/Dimer_metal_binding_domain/3'>Dimer Metal Binding Domain</scene>
 
==DNA/protein interaction==
 
The Upstream activation sequence (<scene name='92/925553/Uas/1'>UAS</scene>) for Gal 4.
 
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.
 
<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.


==See Also==
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
== References ==
<references/>
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Large Structures]]
[[Category: Carey, M]]
[[Category: Harrison, S C]]
[[Category: Marmorstein, R]]
[[Category: Ptashne, M]]
[[Category: Double helix]]
[[Category: Protein-dna complex]]
[[Category: Transcription-dna complex]]

Latest revision as of 17:53, 7 September 2023

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

Structural highlights

1d66 is a 4 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Marmorstein R, Carey M, Ptashne M, Harrison SC. DNA recognition by GAL4: structure of a protein-DNA complex. Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122 doi:http://dx.doi.org/10.1038/356408a0

1d66, resolution 2.70Å

Drag the structure with the mouse to rotate
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