1e6i

From Proteopedia

(Difference between revisions)

Revision as of 10:22, 18 November 2020

Bromodomain from GCN5 complexed with acetylated H4 peptide

Structural highlights

1e6i is a 2 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	1ygh
Gene:	GCN5 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GCN5_YEAST] Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac and H3K36ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation. Operates in concert with certain DNA-binding transcriptional activators such as GCN4 or HAP2/3/4. Its acetyltransferase activity seems to be dependent on the association in different multisubunit complexes. Functions as histone acetyltransferase component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and ADA. 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). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. The ADA histone acetyltransferase complex preferentially acetylates nucleosomal histones H3 (to form H3K14ac and H3K18ac) and H2B, leading to transcription regulation. 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.^[1] ^[2] ^[3]

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

The bromodomain is an approximately 110 amino acid module found in histone acetyltransferases and the ATPase component of certain nucleosome remodelling complexes. We report the crystal structure at 1.9 A resolution of the Saccharomyces cerevisiae Gcn5p bromodomain complexed with a peptide corresponding to residues 15-29 of histone H4 acetylated at the zeta-N of lysine 16. We show that this bromodomain preferentially binds to peptides containing an N:-acetyl lysine residue. Only residues 16-19 of the acetylated peptide interact with the bromodomain. The primary interaction is the N:-acetyl lysine binding in a cleft with the specificity provided by the interaction of the amide nitrogen of a conserved asparagine with the oxygen of the acetyl carbonyl group. A network of water-mediated H-bonds with protein main chain carbonyl groups at the base of the cleft contributes to the binding. Additional side chain binding occurs on a shallow depression that is hydrophobic at one end and can accommodate charge interactions at the other. These findings suggest that the Gcn5p bromodomain may discriminate between different acetylated lysine residues depending on the context in which they are displayed.

The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p.,Owen DJ, Ornaghi P, Yang JC, Lowe N, Evans PR, Ballario P, Neuhaus D, Filetici P, Travers AA EMBO J. 2000 Nov 15;19(22):6141-9. PMID:11080160^[4]

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
↑ Babiarz JE, Halley JE, Rine J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 2006 Mar 15;20(6):700-10. PMID:16543222 doi:http://dx.doi.org/10.1101/gad.1386306
↑ Millar CB, Xu F, Zhang K, Grunstein M. Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. Genes Dev. 2006 Mar 15;20(6):711-22. PMID:16543223 doi:http://dx.doi.org/20/6/711
↑ Owen DJ, Ornaghi P, Yang JC, Lowe N, Evans PR, Ballario P, Neuhaus D, Filetici P, Travers AA. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J. 2000 Nov 15;19(22):6141-9. PMID:11080160 doi:10.1093/emboj/19.22.6141

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/1e6i"

@@ Line 1: / Line 1: @@
 ==Bromodomain from GCN5 complexed with acetylated H4 peptide==
-<StructureSection load='1e6i' size='340' side='right' caption='[[1e6i]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
+<StructureSection load='1e6i' size='340' side='right'caption='[[1e6i]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1e6i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E6I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1e6i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1E6I FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ygh|1ygh]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GCN5 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6i OCA], [http://pdbe.org/1e6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6i RCSB], [http://www.ebi.ac.uk/pdbsum/1e6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6i ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1e6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6i OCA], [http://pdbe.org/1e6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e6i RCSB], [http://www.ebi.ac.uk/pdbsum/1e6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6i ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 1e6i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone acetyltransferase 3D structures|Histone acetyltransferase 3D structures]]
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 39: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Evans, P R]]
 [[Category: Owen, D J]]

1e6i

From Proteopedia

Revision as of 10:22, 18 November 2020

Bromodomain from GCN5 complexed with acetylated H4 peptide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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