7fef: Difference between revisions

Latest revision as of 17:14, 29 November 2023

Crystal structure of AtMBD6 with DNA

Structural highlights

7fef is a 3 chain structure with sequence from Arabidopsis thaliana and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.39Å
Ligands:	5CM
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]

References

↑ 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:https://dx.doi.org/10.1046/j.1365-313x.2003.01756.x
↑ 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:https://dx.doi.org/10.1104/pp.103.026708
↑ 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:https://dx.doi.org/10.1023/B:PLAN.0000019118.56822.a9
↑ 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:https://dx.doi.org/10.1016/j.molcel.2008.11.009
↑ 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:https://dx.doi.org/10.1007/s12038-016-9658-1

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OCA

[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:https://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:https://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:https://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:https://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:https://dx.doi.org/10.1007/s12038-016-9658-1

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[7fef]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FEF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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]] 2.39&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=7fef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fef OCA], [https://pdbe.org/7fef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fef RCSB], [https://www.ebi.ac.uk/pdbsum/7fef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fef ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MBD6_ARATH 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).<ref>PMID:12787239</ref> <ref>PMID:14605234</ref> <ref>PMID:15010609</ref> <ref>PMID:19061642</ref> <ref>PMID:28229965</ref>
+[https://www.uniprot.org/uniprot/MBD6_ARATH 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).<ref>PMID:12787239</ref> <ref>PMID:14605234</ref> <ref>PMID:15010609</ref> <ref>PMID:19061642</ref> <ref>PMID:28229965</ref>
+==See Also==
+*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
 == References ==
 <references/>

7fef: Difference between revisions

Latest revision as of 17:14, 29 November 2023

Crystal structure of AtMBD6 with DNA

Structural highlights

Function

See Also

References

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