7d8k

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Solution structure of the methyl-CpG binding domain of MBD6 from Arabidopsis thaliana

Structural highlights

7d8k is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MBD6_ARATH Transcriptional regulator that binds CpG, CpNpN and CpNpG (N is A, T, or C) islands in promoters regardless the DNA methylation status. Plays probably a role in gene silencing. May associate with histone deacetylase proteins (HDAC). Required for nucleolar dominance that consist in the silencing of rRNA genes inherited from one progenitor in genetic hybrids. Recruited to rRNA genes in a DRM2-dependent manner. Maintains gene silencing by interacting with RNA binding proteins (e.g. NTF2, RPS2C, HDA6 and AGO4) and by regulating DNA methylation status (PubMed:28229965).[1] [2] [3] [4] [5]

Publication Abstract from PubMed

Cytosine methylation is an epigenetic modification essential for formation of mature heterochromatin, gene silencing, and genomic stability. In plants, methylation occurs not only at cytosine bases in CpG but also in CpHpG and CpHpH contexts, where H denotes A, T, or C. Methyl-CpG binding domain (MBD) proteins, which recognize symmetrical methyl-CpG dinucleotides and act as gene repressors in mammalian cells, are also present in plant cells, although their structural and functional properties still remain poorly understood. To fill this gap, in this study, we determined the solution structure of the MBD domain of the MBD6 protein from Arabidopsis thaliana and investigated its binding properties to methylated DNA by binding assays and an in-depth NMR spectroscopic analysis. The AtMBD6 MBD domain folds into a canonical MBD structure in line with its binding specificity toward methyl-CpG and possesses a DNA binding interface similar to mammalian MBD domains. Intriguingly, however, the binding affinity of the AtMBD6 MBD domain toward methyl-CpG-containing DNA was found to be much lower than that of known mammalian MBD domains. The main difference arises from the absence of positively charged residues in AtMBD6 that supposedly interact with the DNA backbone as seen in mammalian MBD/methyl-CpG-containing DNA complexes. Taken together, we have established a structural basis for methyl-CpG recognition by AtMBD6 to develop a deeper understanding how MBD proteins work as mediators of epigenetic signals in plant cells.

Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana.,Mahana Y, Ohki I, Walinda E, Morimoto D, Sugase K, Shirakawa M ACS Omega. 2022 Jan 19;7(4):3212-3221. doi: 10.1021/acsomega.1c04917. eCollection, 2022 Feb 1. PMID:35128234[6]

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

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Citations
1 reviews cite this structure
The Role of Hydrogen Sulfide (H<sub>2</sub>S) in Epigenetic Regulation of Neurodegenerative Diseases: A Systematic Review.
Dogaru et al. (2023)
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3 other articles
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See Also

References

  1. ↑ Zemach A, Grafi G. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J. 2003 Jun;34(5):565-72. doi: 10.1046/j.1365-313x.2003.01756.x. PMID:12787239 doi:http://dx.doi.org/10.1046/j.1365-313x.2003.01756.x
  2. ↑ Ito M, Koike A, Koizumi N, Sano H. Methylated DNA-binding proteins from Arabidopsis. Plant Physiol. 2003 Dec;133(4):1747-54. doi: 10.1104/pp.103.026708. Epub 2003 Nov, 6. PMID:14605234 doi:http://dx.doi.org/10.1104/pp.103.026708
  3. ↑ Scebba F, Bernacchia G, De Bastiani M, Evangelista M, Cantoni RM, Cella R, Locci MT, Pitto L. Arabidopsis MBD proteins show different binding specificities and nuclear localization. Plant Mol Biol. 2003 Nov;53(5):715-31. doi: 10.1023/B:PLAN.0000019118.56822.a9. PMID:15010609 doi:http://dx.doi.org/10.1023/B:PLAN.0000019118.56822.a9
  4. ↑ Preuss SB, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KD, Carrington JC, Baulcombe DC, Viegas W, Pikaard CS. Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell. 2008 Dec 5;32(5):673-84. doi: 10.1016/j.molcel.2008.11.009. PMID:19061642 doi:http://dx.doi.org/10.1016/j.molcel.2008.11.009
  5. ↑ Parida AP, Sharma A, Sharma AK. AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins. J Biosci. 2017 Mar;42(1):57-68. doi: 10.1007/s12038-016-9658-1. PMID:28229965 doi:http://dx.doi.org/10.1007/s12038-016-9658-1
  6. ↑ Mahana Y, Ohki I, Walinda E, Morimoto D, Sugase K, Shirakawa M. Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana. ACS Omega. 2022 Jan 19;7(4):3212-3221. doi: 10.1021/acsomega.1c04917. eCollection, 2022 Feb 1. PMID:35128234 doi:http://dx.doi.org/10.1021/acsomega.1c04917

Contents


PDB ID 7d8k

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