1yse

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{{Seed}}
 
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[[Image:1yse.png|left|200px]]
 
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==Solution structure of the MAR-binding domain of SATB1==
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The line below this paragraph, containing "STRUCTURE_1yse", creates the "Structure Box" on the page.
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<StructureSection load='1yse' size='340' side='right'caption='[[1yse]]' 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'>[[1yse]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YSE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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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=1yse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yse OCA], [https://pdbe.org/1yse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yse RCSB], [https://www.ebi.ac.uk/pdbsum/1yse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yse ProSAT]</span></td></tr>
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{{STRUCTURE_1yse| PDB=1yse | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SATB1_HUMAN SATB1_HUMAN] Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma (By similarity). Binds to DNA at special AT-rich sequences, the consensus SATB1-binding sequence (CSBS), at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes (e.g. PML at the MHC-I locus) and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis. Interacts with the unique region (UR) of cytomegalovirus (CMV). Alu-like motifs and SATB1-binding sites provide a unique chromatin context which seems preferentially targeted by the HIV-1 integration machinery. Moreover, HIV-1 Tat may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T-cells by binding to the same domain than HDAC1. Delineates specific epigenetic modifications at target gene loci, directly up-regulating metastasis-associated genes while down-regulating tumor-suppressor genes. Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis.<ref>PMID:1505028</ref> <ref>PMID:9111059</ref> <ref>PMID:9548713</ref> <ref>PMID:10595394</ref> <ref>PMID:11463840</ref> <ref>PMID:12374985</ref> <ref>PMID:12692553</ref> <ref>PMID:15618465</ref> <ref>PMID:15713622</ref> <ref>PMID:16377216</ref> <ref>PMID:16630892</ref> <ref>PMID:17376900</ref> <ref>PMID:17173041</ref> <ref>PMID:18337816</ref> <ref>PMID:19332023</ref> <ref>PMID:19430959</ref> <ref>PMID:19103759</ref> <ref>PMID:19247486</ref>
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== Evolutionary Conservation ==
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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/ys/1yse_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=1yse 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 ==
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SATB1 is a transcriptional regulator controlling the gene expression that is essential in the maturation of the immune T-cell. SATB1 binds to the nuclear matrix attachment regions of DNA, where it recruits histone deacetylase and represses transcription through a local chromatin remodeling. Here we determined the solution structure of the matrix attachment region-binding domain, possessing similarity to the CUT DNA-binding domain, of human SATB1 by NMR spectroscopy. The structure consists of five alpha-helices, in which the N-terminal four are arranged similarly to the four-helix structure of the CUT domain of hepatocyte nuclear factor 6alpha. By an NMR chemical shift perturbation analysis and by surface plasmon resonance analyses of SATB1 mutant proteins, an interface for DNA binding was revealed to be located at the third helix and the surrounding regions. Surface plasmon resonance experiments using groove-specific binding drugs and methylated DNAs indicated that the domain recognizes DNA from the major groove side. These observations suggested that SATB1 possesses a DNA-binding mode similar to that of the POU-specific DNA-binding domain, which is known to share structural similarity to the four-helix CUT domain.
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===Solution structure of the MAR-binding domain of SATB1===
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Solution structure and DNA-binding mode of the matrix attachment region-binding domain of the transcription factor SATB1 that regulates the T-cell maturation.,Yamaguchi H, Tateno M, Yamasaki K J Biol Chem. 2006 Feb 24;281(8):5319-27. Epub 2005 Dec 21. PMID:16371359<ref>PMID:16371359</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_16371359}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1yse" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16371359 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16371359}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1YSE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSE OCA].
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==Reference==
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<ref group="xtra">PMID:16371359</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Yamaguchi, H.]]
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[[Category: Large Structures]]
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[[Category: Yamasaki, K.]]
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[[Category: Yamaguchi H]]
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[[Category: All helical]]
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[[Category: Yamasaki K]]
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[[Category: Dna-binding domain]]
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[[Category: T-cell development]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:52:44 2009''
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Current revision

Solution structure of the MAR-binding domain of SATB1

PDB ID 1yse

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