5gtc

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle

Structural highlights

5gtc is a 11 chain structure with sequence from Homo sapiens and Human gammaherpesvirus 8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H2B1J_HUMAN Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.^[1] ^[2] ^[3] Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.^[4] ^[5] ^[6]

Publication Abstract from PubMed

Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack of methods for site-selectively modifying native chromatin, however, limits our understanding of the functional roles of a specific histone PTM, not as a single mark, but in the intertwined PTM network. Here, we report a synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including acetyl-CoA) under physiological conditions and transfers various acyl groups to the proximate amino groups. Our data suggest that DSH, conjugated with a nucleosome ligand, such as pyrrole-imidazole-polyamide and LANA (latency-associated nuclear antigen)-peptide, promotes both natural (including acetylation, butyrylation, malonylation, and ubiquitination) and non-natural (azido- and phosphoryl labeling) PTMs on histones in recombinant nucleosomes and/or in native chromatin, at lysine residues close to the DSH moiety. To investigate the validity of our method, we used LANA-DSH to promote histone H2B lysine-120 (K120) acylation, the function of which is largely unknown. H2BK120 acetylation and malonylation modulated higher-order chromatin structures by reducing internucleosomal interactions, and this modulation was further enhanced by histone tail acetylation. This approach, therefore, may have versatile applications for dissecting the regulatory mechanisms underlying chromatin function.

Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.,Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M J Am Chem Soc. 2017 Jun 7;139(22):7568-7576. doi: 10.1021/jacs.7b02138. Epub 2017, May 23. PMID:28534629^[7]

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

References

↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M. Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin. J Am Chem Soc. 2017 Jun 7;139(22):7568-7576. doi: 10.1021/jacs.7b02138. Epub 2017, May 23. PMID:28534629 doi:http://dx.doi.org/10.1021/jacs.7b02138

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5gtc"

@@ Line 1: / Line 1: @@
 ==Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle==
-<StructureSection load='5gtc' size='340' side='right' caption='[[5gtc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='5gtc' size='340' side='right'caption='[[5gtc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gtc]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GTC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gtc]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GTC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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]] 2.7&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HIST1H3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5gtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gtc OCA], [https://pdbe.org/5gtc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gtc RCSB], [https://www.ebi.ac.uk/pdbsum/5gtc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gtc ProSAT]</span></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=5gtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gtc OCA], [http://pdbe.org/5gtc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gtc RCSB], [http://www.ebi.ac.uk/pdbsum/5gtc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gtc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>   Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>
+[https://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>   Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arimura, Y]]
+[[Category: Human gammaherpesvirus 8]]
-[[Category: Kanai, M]]
+[[Category: Large Structures]]
-[[Category: Kato, D]]
+[[Category: Arimura Y]]
-[[Category: Kawashima, S A]]
+[[Category: Kanai M]]
-[[Category: Kurumizaka, H]]
+[[Category: Kato D]]
-[[Category: Suto, H]]
+[[Category: Kawashima SA]]
-[[Category: Yamatsugu, K]]
+[[Category: Kurumizaka H]]
-[[Category: Chromatin formation]]
+[[Category: Suto H]]
-[[Category: Dna binding]]
+[[Category: Yamatsugu K]]
-[[Category: Histone fold]]
-[[Category: Nucleosome]]
-[[Category: Nucleus]]
-[[Category: Structural protein-dna complex]]

5gtc

From Proteopedia

Current revision

Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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