9v4o

From Proteopedia

(Difference between revisions)

Current revision

Cryo-EM structure of A. thaliana MET1 with bound SAH

Structural highlights

9v4o 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:	Electron Microscopy, Resolution 2.92Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNMT1_ARATH Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability. Required for proper patterns of CG DNA methylation in dividing cells. Required for MEA promoter methylation in seeds.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

DNA methylation plays critical roles in eukaryotic gene silencing, genome defense, and the suppression of transposable elements. During DNA replication, DNA methylation is diluted and must therefore be restored through maintenance DNA methylation. In plants, in addition to symmetric CG methylation, non-CG methylation is also abundant, with the maintenance of each DNA methylation pattern employing different pathways. Here, we investigate the molecular basis of CG maintenance methylation by plant METHYLTRANSFERASE 1 (MET1), an ortholog of mammalian DNA Methyltransferase 1 (DNMT1). The cryogenic electron microscopy structure of full-length Arabidopsis (Arabidopsis thaliana) MET1 reveals a unique autoinhibitory mechanism that is distinct from that of DNMT1. The structure of the MET1 catalytic domain in complex with hemimethylated substrate DNA suggests specific recognition of hemimethylated CG DNA and reveals the catalytic mechanism. Overall, our study illuminates the molecular basis of MET1 autoinhibition and its preference for hemimethylated DNA substrates.

Structural insights into plant DNA CG methylation maintenance by MET1.,Zhang Z, Li W, Liu Y, Chi C, Nan J, Wang C, Zhu Y, Zhao J, Xue Y, Li Y, Wang P, Zhai J, Du J Plant Cell. 2025 Oct 31;37(11):koaf244. doi: 10.1093/plcell/koaf244. PMID:41082561^[8]

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

References

↑ Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 2002 Dec 2;21(23):6549-59. PMID:12456661 doi:10.1093/emboj/cdf657
↑ Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003 Mar;163(3):1109-22. PMID:12663548 doi:10.1093/genetics/163.3.1109
↑ Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet. 2003 May;34(1):65-9. PMID:12669067 doi:10.1038/ng1138
↑ Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell. 2003 Dec;5(6):891-901. PMID:14667411 doi:10.1016/s1534-5807(03)00361-7
↑ Xiao W, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell. 2006 Apr;18(4):805-14. PMID:16531498 doi:10.1105/tpc.105.038836
↑ Xiao W, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol. 2006 Nov;142(3):1160-8. PMID:17012404 doi:10.1104/pp.106.088849
↑ Kim M, Ohr H, Lee JW, Hyun Y, Fischer RL, Choi Y. Temporal and spatial downregulation of Arabidopsis MET1 activity results in global DNA hypomethylation and developmental defects. Mol Cells. 2008 Dec 31;26(6):611-5 PMID:18820427
↑ Zhang Z, Li W, Liu Y, Chi C, Nan J, Wang C, Zhu Y, Zhao J, Xue Y, Li Y, Wang P, Zhai J, Du J. Structural insights into plant DNA CG methylation maintenance by MET1. Plant Cell. 2025 Oct 31;37(11):koaf244. PMID:41082561 doi:10.1093/plcell/koaf244

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/9v4o"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9v4o is ON HOLD  until Paper Publication
+==Cryo-EM structure of A. thaliana MET1 with bound SAH==
+<StructureSection load='9v4o' size='340' side='right'caption='[[9v4o]], [[Resolution|resolution]] 2.92&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9v4o]] 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=9V4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9V4O FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.92&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9v4o OCA], [https://pdbe.org/9v4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9v4o RCSB], [https://www.ebi.ac.uk/pdbsum/9v4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9v4o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNMT1_ARATH DNMT1_ARATH] Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability. Required for proper patterns of CG DNA methylation in dividing cells. Required for MEA promoter methylation in seeds.<ref>PMID:12456661</ref> <ref>PMID:12663548</ref> <ref>PMID:12669067</ref> <ref>PMID:14667411</ref> <ref>PMID:16531498</ref> <ref>PMID:17012404</ref> <ref>PMID:18820427</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA methylation plays critical roles in eukaryotic gene silencing, genome defense, and the suppression of transposable elements. During DNA replication, DNA methylation is diluted and must therefore be restored through maintenance DNA methylation. In plants, in addition to symmetric CG methylation, non-CG methylation is also abundant, with the maintenance of each DNA methylation pattern employing different pathways. Here, we investigate the molecular basis of CG maintenance methylation by plant METHYLTRANSFERASE 1 (MET1), an ortholog of mammalian DNA Methyltransferase 1 (DNMT1). The cryogenic electron microscopy structure of full-length Arabidopsis (Arabidopsis thaliana) MET1 reveals a unique autoinhibitory mechanism that is distinct from that of DNMT1. The structure of the MET1 catalytic domain in complex with hemimethylated substrate DNA suggests specific recognition of hemimethylated CG DNA and reveals the catalytic mechanism. Overall, our study illuminates the molecular basis of MET1 autoinhibition and its preference for hemimethylated DNA substrates.
-Authors:
+Structural insights into plant DNA CG methylation maintenance by MET1.,Zhang Z, Li W, Liu Y, Chi C, Nan J, Wang C, Zhu Y, Zhao J, Xue Y, Li Y, Wang P, Zhai J, Du J Plant Cell. 2025 Oct 31;37(11):koaf244. doi: 10.1093/plcell/koaf244. PMID:41082561<ref>PMID:41082561</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9v4o" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Du J]]
+[[Category: Li W]]
+[[Category: Liu Y]]
+[[Category: Zhang Z]]

9v4o

From Proteopedia

Current revision

Cryo-EM structure of A. thaliana MET1 with bound SAH

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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