2zkf

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{{Seed}}
 
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[[Image:2zkf.png|left|200px]]
 
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==Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA==
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The line below this paragraph, containing "STRUCTURE_2zkf", creates the "Structure Box" on the page.
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<StructureSection load='2zkf' size='340' side='right'caption='[[2zkf]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2zkf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZKF FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
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<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>
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{{STRUCTURE_2zkf| PDB=2zkf | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zkf OCA], [https://pdbe.org/2zkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zkf RCSB], [https://www.ebi.ac.uk/pdbsum/2zkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zkf ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UHRF1_MOUSE UHRF1_MOUSE] Multidomain protein that acts as a key epigenetic regulator by bridging DNA methylation and chromatin modification. Specifically recognizes and binds hemimethylated DNA at replication forks via its YDG domain and recruits DNMT1 methyltransferase to ensure faithful propagation of the DNA methylation patterns through DNA replication. In addition to its role in maintenance of DNA methylation, also plays a key role in chromatin modification: through its tudor-like regions and PHD-type zinc fingers, specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3) and unmethylated at 'Arg-2' (H3R2me0), respectively, and recruits chromatin proteins. Enriched in pericentric heterochromatin where it recruits different chromatin modifiers required for this chromatin replication. Also localizes to euchromatic regions where it negatively regulates transcription possibly by impacting DNA methylation and histone modifications. Has E3 ubiquitin-protein ligase activity by mediating the ubiquitination of target proteins such as histone H3 and PML. It is still unclear how E3 ubiquitin-protein ligase activity is related to its role in chromatin in vivo. May be involved in DNA repair.<ref>PMID:12084726</ref> <ref>PMID:12058012</ref> <ref>PMID:14993289</ref> <ref>PMID:15361834</ref> <ref>PMID:17994007</ref> <ref>PMID:17673620</ref> <ref>PMID:21489993</ref> <ref>PMID:21268065</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zk/2zkf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zkf ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.
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===Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA===
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Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.,Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M Nature. 2008 Oct 9;455(7214):818-21. Epub 2008 Sep 3. PMID:18772891<ref>PMID:18772891</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2zkf" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18772891}}, adds the Publication Abstract to the page
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*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18772891 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18772891}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2ZKF is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZKF OCA].
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==Reference==
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<ref group="xtra">PMID:18772891</ref><references group="xtra"/>
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[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Arita, K.]]
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[[Category: Arita K]]
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[[Category: Ariyoshi, M.]]
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[[Category: Ariyoshi M]]
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[[Category: Nakamura, Y.]]
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[[Category: Nakamura Y]]
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[[Category: Shirakawa, M.]]
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[[Category: Shirakawa M]]
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[[Category: Tochio, H.]]
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[[Category: Tochio H]]
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[[Category: Cell cycle]]
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[[Category: Developmental protein]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna-binding]]
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[[Category: Ligase]]
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[[Category: Metal-binding]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Protein-dna interaction]]
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[[Category: Transcription]]
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[[Category: Transcription regulation]]
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[[Category: Ubl conjugation]]
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[[Category: Ubl conjugation pathway]]
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[[Category: Zinc]]
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[[Category: Zinc-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:58:06 2009''
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Current revision

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA

PDB ID 2zkf

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