2dy7: Difference between revisions

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-{{Seed}}
-[[Image:2dy7.png|left|200px]]
-<!--
+==Solution structure of the first chromodomain of yeast Chd1==
-The line below this paragraph, containing "STRUCTURE_2dy7", creates the "Structure Box" on the page.
+<StructureSection load='2dy7' size='340' side='right'caption='[[2dy7]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2dy7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DY7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2dy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy7 OCA], [https://pdbe.org/2dy7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy7 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy7 ProSAT]</span></td></tr>
-{{STRUCTURE_2dy7|  PDB=2dy7  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CHD1_YEAST CHD1_YEAST] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.<ref>PMID:10026213</ref> <ref>PMID:10811623</ref> <ref>PMID:12682017</ref> <ref>PMID:14585955</ref> <ref>PMID:15647753</ref> <ref>PMID:16606615</ref> <ref>PMID:16468993</ref> <ref>PMID:17949749</ref> <ref>PMID:17620414</ref> <ref>PMID:17259992</ref> <ref>PMID:18245327</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/dy/2dy7_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=2dy7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem chromodomains. In human CHD1, both chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second chromodomain nor a region containing tandem chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second chromodomains determined individually by NMR. Both chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded beta-sheet followed by a C-terminal alpha-helix. However, an additional helix between the first and second beta-strands, which is found in both of the first chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins.
-===Solution structure of the first chromodomain of yeast Chd1===
+Structural polymorphism of chromodomains in Chd1.,Okuda M, Horikoshi M, Nishimura Y J Mol Biol. 2007 Jan 26;365(4):1047-62. Epub 2006 Oct 14. PMID:17098252<ref>PMID:17098252</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dy7" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17098252}}, adds the Publication Abstract to the page
+*[[Helicase 3D structures|Helicase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17098252 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17098252}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DY7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DY7 OCA].
-==Reference==
-Structural polymorphism of chromodomains in Chd1., Okuda M, Horikoshi M, Nishimura Y, J Mol Biol. 2007 Jan 26;365(4):1047-62. Epub 2006 Oct 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17098252 17098252]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Nishimura Y]]
-[[Category: Nishimura, Y.]]
+[[Category: Okuda M]]
-[[Category: Okuda, M.]]
-[[Category: Chromatin remodeling]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:16:57 2008''