1fp0

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(New page: 200px<br /> <applet load="1fp0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fp0" /> '''SOLUTION STRUCTURE OF THE PHD DOMAIN FROM T...)
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[[Image:1fp0.gif|left|200px]]<br />
 
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<applet load="1fp0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fp0" />
 
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'''SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR'''<br />
 
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==Overview==
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==SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR==
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Plant homeodomain (PHD) domains are found in &gt;400 eukaryotic proteins, many of which are transcriptional regulators. Naturally occurring point, mutations or deletions of this domain contribute to a variety of human, diseases, including ATRX syndrome, myeloid leukemias and autoimmune, dysfunction. Here we report the first structural characterization of a PHD, domain. Our studies reveal that the PHD domain from KAP-1 corepressor, binds zinc in a cross-brace topology between anti-parallel ss-strands, reminiscent of RING (really interesting new gene) domains. Using a, mutational analysis, we define the structural features required for, transcriptional repression by KAP-1 and explain naturally occurring, disease-causing mutations in PHD domains of other proteins. From a, comparison of this PHD structure with previously reported RING and LIM, (Lin11/Isl-1/Mec-3) structures, we infer sequence determinants that allow, discrimination among PHD, RING and LIM motifs.
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<StructureSection load='1fp0' size='340' side='right'caption='[[1fp0]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1fp0]] 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=1FP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FP0 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">Solution NMR</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=ZN:ZINC+ION'>ZN</scene></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=1fp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fp0 OCA], [https://pdbe.org/1fp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fp0 RCSB], [https://www.ebi.ac.uk/pdbsum/1fp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fp0 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TIF1B_HUMAN TIF1B_HUMAN] Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs). Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. Recruitment of SETDB1 induces heterochromatinization. May play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. Also corepressor for ERBB4. Inhibits E2F1 activity by stimulating E2F1-HDAC1 complex formation and inhibiting E2F1 acetylation. May serve as a partial backup to prevent E2F1-mediated apoptosis in the absence of RB1. Important regulator of CDKN1A/p21(CIP1). Has E3 SUMO-protein ligase activity toward itself via its PHD-type zinc finger. Also specifically sumoylates IRF7, thereby inhibiting its transactivation activity. Ubiquitinates p53/TP53 leading to its proteosomal degradation; the function is enhanced by MAGEC2 and MAGEA2, and possibly MAGEA3 and MAGEA6.<ref>PMID:8769649</ref> <ref>PMID:9016654</ref> <ref>PMID:10347202</ref> <ref>PMID:11959841</ref> <ref>PMID:15882967</ref> <ref>PMID:16107876</ref> <ref>PMID:17178852</ref> <ref>PMID:16862143</ref> <ref>PMID:17079232</ref> <ref>PMID:17704056</ref> <ref>PMID:17942393</ref> <ref>PMID:18082607</ref> <ref>PMID:18060868</ref> <ref>PMID:20858735</ref> <ref>PMID:20864041</ref> <ref>PMID:20424263</ref> <ref>PMID:21940674</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/fp/1fp0_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=1fp0 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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Plant homeodomain (PHD) domains are found in &gt;400 eukaryotic proteins, many of which are transcriptional regulators. Naturally occurring point mutations or deletions of this domain contribute to a variety of human diseases, including ATRX syndrome, myeloid leukemias and autoimmune dysfunction. Here we report the first structural characterization of a PHD domain. Our studies reveal that the PHD domain from KAP-1 corepressor binds zinc in a cross-brace topology between anti-parallel ss-strands reminiscent of RING (really interesting new gene) domains. Using a mutational analysis, we define the structural features required for transcriptional repression by KAP-1 and explain naturally occurring, disease-causing mutations in PHD domains of other proteins. From a comparison of this PHD structure with previously reported RING and LIM (Lin11/Isl-1/Mec-3) structures, we infer sequence determinants that allow discrimination among PHD, RING and LIM motifs.
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==About this Structure==
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Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.,Capili AD, Schultz DC, RauscherIII FJ, Borden KL EMBO J. 2001 Jan 15;20(1-2):165-77. PMID:11226167<ref>PMID:11226167</ref>
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1FP0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FP0 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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Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains., Capili AD, Schultz DC, RauscherIII FJ, Borden KL, EMBO J. 2001 Jan 15;20(1-2):165-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11226167 11226167]
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</div>
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<div class="pdbe-citations 1fp0" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Borden, K.L.B.]]
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[[Category: Borden KLB]]
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[[Category: Capili, A.D.]]
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[[Category: Capili AD]]
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[[Category: III, F.J.Rauscher.]]
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[[Category: Rauscher III FJ]]
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[[Category: Schultz, D.C.]]
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[[Category: Schultz DC]]
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[[Category: ZN]]
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[[Category: c3hc4 type zinc binding domain]]
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[[Category: nmr-structure]]
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[[Category: phd domain]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 16:55:52 2007''
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Current revision

SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR

PDB ID 1fp0

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