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{{STRUCTURE_2ada| PDB=2ada  | SCENE= }}
{{Gal4 practice page}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
==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=''>
== 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.
Gal4 has lots of <scene name='89/891376/Basic_aas/2'>basic amino acids</scene> that interact with DNA.


===ADENOSINE DEAMINASE===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div>


Adenosine deaminase is involved in the degradation of purine nucleotides.  It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency.  Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref>  The active site contains a <scene name='36/365334/Zinc_cofactor/3'>Zinc cofactor</scene>, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside.  The zinc is coordinated to <scene name='36/365334/Histidine_residues/1'>three Histidine residues</scene> and <scene name='36/365334/Aspartic_acid_residue/1'>an aspartic acid residue</scene>. 
==See Also==
 
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]
The transition state analogue held in place mostly by polar interactions.  The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc.  Nine hydrogen bonds stabilize the transition state-enzyme complex. 
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
 
== References ==
ADA is very stereoselective for the 6R isomer.  This specificity is due to the location of the catalytic zinc, <scene name='36/365334/Asp_295/1'>Asp295</scene> and <scene name='36/365334/His_238/2'>His238</scene>.  Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues.  The proposed catalytic mechanism has <scene name='36/365334/Asp_295/1'>Asp295</scene> act as a general base, while the zinc acts as an electrophile to activate the water molecule.  <scene name='36/365334/His_238/2'>His238</scene> orients the water and stabilizes the charge of the attacking hydroxide.  The protonated <scene name='36/365334/Glu217/2'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.
 
Reference
<references/>
<references/>
__TOC__
</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]]

Revision as of 15:55, 7 September 2023

This Sandbox is Reserved from 09/01/2021 through 12/01/2021 for use in Che 462 taught by Ann Taylor at Wabash College, Crawfordsville, IN USA. This reservation includes Sandbox Reserved 1683 through Sandbox Reserved 1689.
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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. Gal4 has lots of that interact with DNA.

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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Ann Taylor, Refayat Ahsen
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