2ky8: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence==
==Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence==
<StructureSection load='2ky8' size='340' side='right' caption='[[2ky8]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='2ky8' size='340' side='right'caption='[[2ky8]]' scene=''>
== Structural highlights ==
== Structural highlights ==
[[2ky8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY8 OCA]. <br>
<table><tr><td colspan='2'>[[2ky8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KY8 FirstGlance]. <br>
<b>Related:</b> [[3c2i|3c2i]], [[1ig4|1ig4]]<br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
<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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TED:5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO-4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>TED</scene></td></tr>
== Publication Abstract from PubMed ==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ky8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ky8 OCA], [https://pdbe.org/2ky8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ky8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ky8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ky8 ProSAT]</span></td></tr>
The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal beta-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the rho-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the rho-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central beta-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG.
</table>
 
== Function ==
Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence.,Scarsdale JN, Webb HD, Ginder GD, Williams DC Jr Nucleic Acids Res. 2011 Apr 29. PMID:21531701<ref>PMID:21531701</ref>
[https://www.uniprot.org/uniprot/Q5EFL0_CHICK Q5EFL0_CHICK]


From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
==See Also==
== References ==
*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Scarsdale, J N.]]
[[Category: Large Structures]]
[[Category: Williams, D C.]]
[[Category: Scarsdale Jr JN]]
[[Category: Dna binding domain]]
[[Category: Williams Jr DC]]
[[Category: Transcription-dna complex]]

Latest revision as of 09:50, 1 May 2024

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequenceSolution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence

Structural highlights

2ky8 is a 3 chain structure with sequence from Gallus gallus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5EFL0_CHICK

See Also

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2ky8&oldid=4136060"