7vz2

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of chromodomain of Arabidopsis LHP1

Structural highlights

7vz2 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LHP1_ARATH Structural component of heterochromatin involved in gene repression, including several floral homeotic genes and FLT that regulates flowering time. Required for maintenance of vernalization-induced repression of FLC. As part of the PRC1-like complex, recognizes and binds histone H3 tails methylated at 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me), leading to epigenetic repression. PcG PRC1 complex maintains the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Transcriptional repressor that binds DNA on GAGA-like motif and 5'-(A/G/T)AACCCTA(A/G)-3' consensus motif in the promoters of target genes. Recognizes and binds histone H3 tails methylated at 'Lys-27' (H3K27me) but depleted in active histone marks such as H3K4me, leading to epigenetic repression. When in complex with LHP1, recognizes and binds histone H3 tails methylated at 'Lys-4' (H3K4me) and 'Lys-27' (H3K27me), mostly corresponding to stress-responsive genes (PubMed:27495811).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides, and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, while it exhibited no binding or weak binding to unmodified or mono-methylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Pc proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.

Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain.,Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J J Biol Chem. 2022 Jan 21:101623. doi: 10.1016/j.jbc.2022.101623. PMID:35074427^[8]

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

References

↑ Gaudin V, Libault M, Pouteau S, Juul T, Zhao G, Lefebvre D, Grandjean O. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development. 2001 Dec;128(23):4847-58. doi: 10.1242/dev.128.23.4847. PMID:11731464 doi:http://dx.doi.org/10.1242/dev.128.23.4847
↑ Kotake T, Takada S, Nakahigashi K, Ohto M, Goto K. Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol. 2003 Jun;44(6):555-64. doi: 10.1093/pcp/pcg091. PMID:12826620 doi:http://dx.doi.org/10.1093/pcp/pcg091
↑ Kim JH, Durrett TP, Last RL, Jander G. Characterization of the Arabidopsis TU8 glucosinolate mutation, an allele of TERMINAL FLOWER2. Plant Mol Biol. 2004 Mar;54(5):671-82. PMID:15356387 doi:http://dx.doi.org/10.1023/B:PLAN.0000040897.49151.98
↑ Mylne JS, Barrett L, Tessadori F, Mesnage S, Johnson L, Bernatavichute YV, Jacobsen SE, Fransz P, Dean C. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5012-7. Epub 2006 Mar 20. PMID:16549797 doi:http://dx.doi.org/0507427103
↑ Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM. Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet. 2006 Jun;38(6):706-10. doi: 10.1038/ng1795. Epub 2006 May 7. PMID:16682972 doi:http://dx.doi.org/10.1038/ng1795
↑ Xu L, Shen WH. Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis. Curr Biol. 2008 Dec 23;18(24):1966-71. doi: 10.1016/j.cub.2008.11.019. PMID:19097900 doi:http://dx.doi.org/10.1016/j.cub.2008.11.019
↑ Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Herin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V. The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes. Plant Cell. 2016 Sep;28(9):2197-2211. doi: 10.1105/tpc.16.00244. Epub 2016 Aug 5. PMID:27495811 doi:http://dx.doi.org/10.1105/tpc.16.00244
↑ Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem. 2022 Jan 21:101623. doi: 10.1016/j.jbc.2022.101623. PMID:35074427 doi:http://dx.doi.org/10.1016/j.jbc.2022.101623

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/7vz2"

Categories: Arabidopsis thaliana | Large Structures | Liu Y | Min J

@@ Line 3: / Line 3: @@
 <StructureSection load='7vz2' size='340' side='right'caption='[[7vz2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7vz2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VZ2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7vz2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VZ2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></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=7vz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vz2 OCA], [https://pdbe.org/7vz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vz2 RCSB], [https://www.ebi.ac.uk/pdbsum/7vz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vz2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/LHP1_ARATH LHP1_ARATH]] Structural component of heterochromatin involved in gene repression, including several floral homeotic genes and FLT that regulates flowering time. Required for maintenance of vernalization-induced repression of FLC. As part of the PRC1-like complex, recognizes and binds histone H3 tails methylated at 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me), leading to epigenetic repression. PcG PRC1 complex maintains the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Transcriptional repressor that binds DNA on GAGA-like motif and 5'-(A/G/T)AACCCTA(A/G)-3' consensus motif in the promoters of target genes. Recognizes and binds histone H3 tails methylated at 'Lys-27' (H3K27me) but depleted in active histone marks such as H3K4me, leading to epigenetic repression. When in complex with LHP1, recognizes and binds histone H3 tails methylated at 'Lys-4' (H3K4me) and 'Lys-27' (H3K27me), mostly corresponding to stress-responsive genes (PubMed:27495811).<ref>PMID:11731464</ref> <ref>PMID:12826620</ref> <ref>PMID:15356387</ref> <ref>PMID:16549797</ref> <ref>PMID:16682972</ref> <ref>PMID:19097900</ref> <ref>PMID:27495811</ref>
+[https://www.uniprot.org/uniprot/LHP1_ARATH LHP1_ARATH] Structural component of heterochromatin involved in gene repression, including several floral homeotic genes and FLT that regulates flowering time. Required for maintenance of vernalization-induced repression of FLC. As part of the PRC1-like complex, recognizes and binds histone H3 tails methylated at 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me), leading to epigenetic repression. PcG PRC1 complex maintains the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Transcriptional repressor that binds DNA on GAGA-like motif and 5'-(A/G/T)AACCCTA(A/G)-3' consensus motif in the promoters of target genes. Recognizes and binds histone H3 tails methylated at 'Lys-27' (H3K27me) but depleted in active histone marks such as H3K4me, leading to epigenetic repression. When in complex with LHP1, recognizes and binds histone H3 tails methylated at 'Lys-4' (H3K4me) and 'Lys-27' (H3K27me), mostly corresponding to stress-responsive genes (PubMed:27495811).<ref>PMID:11731464</ref> <ref>PMID:12826620</ref> <ref>PMID:15356387</ref> <ref>PMID:16549797</ref> <ref>PMID:16682972</ref> <ref>PMID:19097900</ref> <ref>PMID:27495811</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Liu, Y]]
+[[Category: Liu Y]]
-[[Category: Min, J]]
+[[Category: Min J]]
-[[Category: Transcription]]

7vz2

From Proteopedia

Current revision

Crystal structure of chromodomain of Arabidopsis LHP1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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