1k61

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[[Image:1k61.gif|left|200px]]
 
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==MATALPHA2 HOMEODOMAIN BOUND TO DNA==
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The line below this paragraph, containing "STRUCTURE_1k61", creates the "Structure Box" on the page.
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<StructureSection load='1k61' size='340' side='right'caption='[[1k61]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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</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>
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<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>
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{{STRUCTURE_1k61| PDB=1k61 | SCENE= }}
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<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>
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</table>
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'''MATALPHA2 HOMEODOMAIN BOUND TO DNA'''
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== Function ==
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[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>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k6/1k61_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== 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.
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.
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==About this Structure==
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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>
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1K61 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K61 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/12466549 12466549]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1k61" style="background-color:#fffaf0;"></div>
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[[Category: Aishima, J.]]
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== References ==
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[[Category: Gan, H H.]]
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<references/>
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[[Category: Gitti, R K.]]
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__TOC__
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[[Category: Noah, J E.]]
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</StructureSection>
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[[Category: Schlick, T.]]
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[[Category: Large Structures]]
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[[Category: Wolberger, C.]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Homeodomain]]
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[[Category: Aishima J]]
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[[Category: Hoogsteen base pair]]
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[[Category: Gan HH]]
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[[Category: Protein-dna complex]]
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[[Category: Gitti RK]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:21:05 2008''
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[[Category: Noah JE]]
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[[Category: Schlick T]]
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[[Category: Wolberger C]]

Current revision

MATALPHA2 HOMEODOMAIN BOUND TO DNA

PDB ID 1k61

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