1k61: Difference between revisions
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New page: left|200px<br /><applet load="1k61" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k61, resolution 2.10Å" /> '''MATALPHA2 HOMEODOMAI... |
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== | ==MATALPHA2 HOMEODOMAIN BOUND TO DNA== | ||
Hoogsteen base pairs within duplex DNA typically are only observed in | <StructureSection load='1k61' size='340' side='right'caption='[[1k61]], [[Resolution|resolution]] 2.10Å' 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]] 2.1Å</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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1k61" style="background-color:#fffaf0;"></div> | ||
[[Category: Aishima | == References == | ||
[[Category: Gan | <references/> | ||
[[Category: Gitti | __TOC__ | ||
[[Category: Noah | </StructureSection> | ||
[[Category: Schlick | [[Category: Large Structures]] | ||
[[Category: Wolberger | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Aishima J]] | |||
[[Category: Gan HH]] | |||
[[Category: Gitti RK]] | |||
[[Category: Noah JE]] | |||
[[Category: Schlick T]] | |||
[[Category: Wolberger C]] | |||
