1k61: Difference between revisions

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-[[Image:1k61.png|left|200px]]
-{{STRUCTURE_1k61|  PDB=1k61  |  SCENE=  }}
+==MATALPHA2 HOMEODOMAIN BOUND TO DNA==
+<StructureSection load='1k61' size='340' side='right'caption='[[1k61]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k61]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K61 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</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=1k61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k61 OCA], [https://pdbe.org/1k61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k61 RCSB], [https://www.ebi.ac.uk/pdbsum/1k61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k61 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MTAL2_YEAST MTAL2_YEAST] Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Transcriptional corepressor that binds cooperatively with MCM1 to a 31-basepair DNA sequence termed the a-specific gene (asg) operator, to repress the transcription of a-cell-specific genes. Additionally, in a/alpha diploid cells, binds cooperatively with the A1 protein to a 21-basepair DNA sequence termed the haploid-specific gene (hsg) operator, to repress transcription of haploid-specific genes and of MATALPHA1.<ref>PMID:8664541</ref>
+== 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/k6/1k61_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=1k61 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 A resolution structure of the MATalpha2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson-Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain-DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein-DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.
-===MATALPHA2 HOMEODOMAIN BOUND TO DNA===
+A Hoogsteen base pair embedded in undistorted B-DNA.,Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C Nucleic Acids Res. 2002 Dec 1;30(23):5244-52. PMID:12466549<ref>PMID:12466549</ref>
-{{ABSTRACT_PUBMED_12466549}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1k61" style="background-color:#fffaf0;"></div>
-[[1k61]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K61 OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:012466549</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Aishima, J.]]
+[[Category: Large Structures]]
-[[Category: Gan, H H.]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Gitti, R K.]]
+[[Category: Aishima J]]
-[[Category: Noah, J E.]]
+[[Category: Gan HH]]
-[[Category: Schlick, T.]]
+[[Category: Gitti RK]]
-[[Category: Wolberger, C.]]
+[[Category: Noah JE]]
-[[Category: Homeodomain]]
+[[Category: Schlick T]]
-[[Category: Hoogsteen base pair]]
+[[Category: Wolberger C]]
-[[Category: Protein-dna complex]]
-[[Category: Transcription-dna complex]]