2o49: Difference between revisions

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[[Image:2o49.png|left|200px]]


{{STRUCTURE_2o49| PDB=2o49 | SCENE= }}
==Crystal Structure of the N-terminal CUT domain of SATB1 Bound to Matrix Attachment Region DNA==
<StructureSection load='2o49' size='340' side='right'caption='[[2o49]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2o49]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O49 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&#8491;</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=2o49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o49 OCA], [https://pdbe.org/2o49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o49 RCSB], [https://www.ebi.ac.uk/pdbsum/2o49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o49 ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== 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/o4/2o49_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=2o49 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Special AT-rich sequence binding protein 1 (SATB1) regulates gene expression essential in immune T-cell maturation and switching of fetal globin species, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin remodeling. Previously we have revealed a five-helix structure of the N-terminal CUT domain, which is essentially the folded region in the MAR-binding domain, of human SATB1 by NMR. Here we determined crystal structure of the complex of the CUT domain and a MAR DNA, in which the third helix of the CUT domain deeply enters the major groove of DNA in the B-form. Bases of 5'-CTAATA-3' sequence are contacted by this helix, through direct and water-mediated hydrogen bonds and apolar and van der Waals contacts. Mutations at conserved base-contacting residues, Gln402 and Gly403, reduced the DNA-binding activity, which confirmed the importance of the observed interactions involving these residues. A significant number of equivalent contacts are observed also for typically four-helix POU-specific domains of POU-homologous proteins, indicating that these domains share a common framework of the DNA-binding mode, recognizing partially similar DNA sequences.


===Crystal Structure of the N-terminal CUT domain of SATB1 Bound to Matrix Attachment Region DNA===
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.,Yamasaki K, Akiba T, Yamasaki T, Harata K Nucleic Acids Res. 2007;35(15):5073-84. Epub 2007 Jul 25. PMID:17652321<ref>PMID:17652321</ref>


{{ABSTRACT_PUBMED_17652321}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 2o49" style="background-color:#fffaf0;"></div>
[[2o49]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O49 OCA].
== References ==
 
<references/>
==Reference==
__TOC__
<ref group="xtra">PMID:017652321</ref><references group="xtra"/>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Akiba, T.]]
[[Category: Large Structures]]
[[Category: Harata, K.]]
[[Category: Akiba T]]
[[Category: Yamasaki, K.]]
[[Category: Harata K]]
[[Category: Protein-dna complex]]
[[Category: Yamasaki K]]
[[Category: Transcription]]
[[Category: Transcription-dna complex]]
Retrieved from "https://proteopedia.org/2o49"