3gx4: Difference between revisions

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{{Seed}}
[[Image:3gx4.png|left|200px]]


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==Crystal Structure Analysis of S. Pombe ATL in complex with DNA==
The line below this paragraph, containing "STRUCTURE_3gx4", creates the "Structure Box" on the page.
<StructureSection load='3gx4' size='340' side='right'caption='[[3gx4]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3gx4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GX4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
{{STRUCTURE_3gx4|  PDB=3gx4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gx4 OCA], [https://pdbe.org/3gx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gx4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gx4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ATL1_SCHPO ATL1_SCHPO] Acts as a DNA damage recognition factor. Required for DNA repair from mutagenic O(6)-alkylguanine adducts. Binds O(6)-alkylguanine lesions providing a signal for other DNA repair pathways.
== 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/gx/3gx4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3gx4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O(6)-methylguanine or cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.


===Crystal Structure Analysis of S. Pombe ATL in complex with DNA===
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.,Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ, Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF, Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams DM, Fried MG, Margison GP, Pegg AE, Tainer JA Nature. 2009 Jun 11;459(7248):808-13. PMID:19516334<ref>PMID:19516334</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_19516334}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3gx4" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19516334 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19516334}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3GX4 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GX4 OCA].
 
==Reference==
<ref group="xtra">PMID:19516334</ref><references group="xtra"/>
[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Arvai, A S.]]
[[Category: Arvai AS]]
[[Category: Tainer, J A.]]
[[Category: Tainer JA]]
[[Category: Tubbs, J L.]]
[[Category: Tubbs JL]]
[[Category: Alkylated dna damage repair methylguanine]]
[[Category: Dna binding protein/dna complex]]
[[Category: Dna damage]]
[[Category: Dna repair]]
[[Category: Dna-binding]]
 
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