2h1e

From Proteopedia

(Difference between revisions)

Current revision

Tandem chromodomains of budding yeast CHD1

Structural highlights

2h1e is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Double chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint their differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.

Molecular implications of evolutionary differences in CHD double chromodomains.,Flanagan JF, Blus BJ, Kim D, Clines KL, Rastinejad F, Khorasanizadeh S J Mol Biol. 2007 Jun 1;369(2):334-42. Epub 2007 Mar 19. PMID:17433364^[12]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Grant PA, Eberharter A, John S, Cook RG, Turner BM, Workman JL. Expanded lysine acetylation specificity of Gcn5 in native complexes. J Biol Chem. 1999 Feb 26;274(9):5895-900. PMID:10026213
↑ Tran HG, Steger DJ, Iyer VR, Johnson AD. The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 2000 May 15;19(10):2323-31. PMID:10811623 doi:http://dx.doi.org/10.1093/emboj/19.10.2323
↑ Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 2003 Apr 15;22(8):1846-56. PMID:12682017 doi:http://dx.doi.org/10.1093/emboj/cdg179
↑ Robinson KM, Schultz MC. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol Cell Biol. 2003 Nov;23(22):7937-46. PMID:14585955
↑ Pray-Grant MG, Daniel JA, Schieltz D, Yates JR 3rd, Grant PA. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature. 2005 Jan 27;433(7024):434-8. Epub 2005 Jan 12. PMID:15647753 doi:http://dx.doi.org/nature03242
↑ Stockdale C, Flaus A, Ferreira H, Owen-Hughes T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem. 2006 Jun 16;281(24):16279-88. Epub 2006 Apr 10. PMID:16606615 doi:http://dx.doi.org/10.1074/jbc.M600682200
↑ Xella B, Goding C, Agricola E, Di Mauro E, Caserta M. The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol Microbiol. 2006 Mar;59(5):1531-41. PMID:16468993 doi:http://dx.doi.org/10.1111/j.1365-2958.2005.05031.x
↑ Ferreira H, Flaus A, Owen-Hughes T. Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J Mol Biol. 2007 Nov 30;374(3):563-79. Epub 2007 Sep 26. PMID:17949749 doi:http://dx.doi.org/10.1016/j.jmb.2007.09.059
↑ Biswas D, Dutta-Biswas R, Stillman DJ. Chd1 and yFACT act in opposition in regulating transcription. Mol Cell Biol. 2007 Sep;27(18):6279-87. Epub 2007 Jul 9. PMID:17620414 doi:http://dx.doi.org/10.1128/MCB.00978-07
↑ Jones HS, Kawauchi J, Braglia P, Alen CM, Kent NA, Proudfoot NJ. RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol. 2007 Feb;14(2):123-30. Epub 2007 Jan 28. PMID:17259992 doi:http://dx.doi.org/10.1038/nsmb1199
↑ Biswas D, Takahata S, Xin H, Dutta-Biswas R, Yu Y, Formosa T, Stillman DJ. A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae. Genetics. 2008 Feb;178(2):649-59. doi: 10.1534/genetics.107.084202. Epub 2008 Feb, 1. PMID:18245327 doi:http://dx.doi.org/10.1534/genetics.107.084202
↑ Flanagan JF, Blus BJ, Kim D, Clines KL, Rastinejad F, Khorasanizadeh S. Molecular implications of evolutionary differences in CHD double chromodomains. J Mol Biol. 2007 Jun 1;369(2):334-42. Epub 2007 Mar 19. PMID:17433364 doi:10.1016/j.jmb.2007.03.024

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2h1e"

Categories: Large Structures | Saccharomyces cerevisiae | Flanagan IV JF | Khorasanizadeh S

@@ Line 3: / Line 3: @@
 <StructureSection load='2h1e' size='340' side='right'caption='[[2h1e]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2h1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2h1e]] is a 2 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=2H1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H1E FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b2t|2b2t]], [[2b2u|2b2u]], [[2b2v|2b2v]], [[2b2w|2b2w]], [[2b2y|2b2y]], [[1kne|1kne]], [[1pdq|1pdq]], [[1guw|1guw]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CHD1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2h1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h1e OCA], [https://pdbe.org/2h1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h1e RCSB], [https://www.ebi.ac.uk/pdbsum/2h1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h1e ProSAT]</span></td></tr>
 </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>
+[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]]
@@ Line 36: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: IV, J F.Flanagan]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Khorasanizadeh, S]]
+[[Category: Flanagan IV JF]]
-[[Category: Chd1]]
+[[Category: Khorasanizadeh S]]
-[[Category: Chromodomain]]
-[[Category: Hydrolase]]
-[[Category: Tandem chromodomain]]
-[[Category: Three-stranded antiparallel b-sheet]]

2h1e

From Proteopedia

Current revision

Tandem chromodomains of budding yeast CHD1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox