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| | ==CpG specific methyltransferase in complex with target DNA== | | ==CpG specific methyltransferase in complex with target DNA== |
| - | <StructureSection load='4dkj' size='340' side='right' caption='[[4dkj]], [[Resolution|resolution]] 2.15Å' scene=''> | + | <StructureSection load='4dkj' size='340' side='right'caption='[[4dkj]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4dkj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_penetrans_hf-2 Mycoplasma penetrans hf-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DKJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4dkj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Malacoplasma_penetrans_HF-2 Malacoplasma penetrans HF-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DKJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.15Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C37:5-FLUORO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C37</scene></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>, <scene name='pdbligand=C37:5-FLUORO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C37</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3pt6|3pt6]], [[3pt9|3pt9]], [[3pta|3pta]], [[1mht|1mht]], [[2c7p|2c7p]], [[4da4|4da4]]</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=4dkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkj OCA], [https://pdbe.org/4dkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dkj RCSB], [https://www.ebi.ac.uk/pdbsum/4dkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkj ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MYPE4940 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272633 Mycoplasma penetrans HF-2])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dkj RCSB], [http://www.ebi.ac.uk/pdbsum/4dkj PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q8EVR5_MALP2 Q8EVR5_MALP2] |
| - | Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-A resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.
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| - | CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.,Wojciechowski M, Czapinska H, Bochtler M Proc Natl Acad Sci U S A. 2012 Dec 17. PMID:23248272<ref>PMID:23248272</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mycoplasma penetrans hf-2]] | + | [[Category: Large Structures]] |
| - | [[Category: Bochtler, M]] | + | [[Category: Malacoplasma penetrans HF-2]] |
| - | [[Category: Czapinska, H]] | + | [[Category: Bochtler M]] |
| - | [[Category: Wojciechowski, M]] | + | [[Category: Czapinska H]] |
| - | [[Category: C-5 cytosine-specific dna methylase]]
| + | [[Category: Wojciechowski M]] |
| - | [[Category: C5-methylcytosine]]
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| - | [[Category: Cg-specificity]]
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| - | [[Category: Cpg sequence]]
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| - | [[Category: Cytosine c5-methylation]]
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| - | [[Category: Dna binding]]
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| - | [[Category: Dna intercalation]]
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| - | [[Category: Intracellular]]
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| - | [[Category: Nucleotide flipping]]
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| - | [[Category: S-adenosyl-l-methionine-dependent methyltransferase]]
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| - | [[Category: Transferase-dna complex]]
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