3ubt: Difference between revisions

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 ==Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA==
-<StructureSection load='3ubt' size='340' side='right' caption='[[3ubt]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3ubt' size='340' side='right'caption='[[3ubt]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ubt]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aegyptius"_trevisan_1889 "bacillus aegyptius" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UBT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ubt]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_aegyptius Haemophilus aegyptius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UBT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.502&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">haeIIIM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197575 "Bacillus aegyptius" Trevisan 1889])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ubt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubt OCA], [https://pdbe.org/3ubt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ubt RCSB], [https://www.ebi.ac.uk/pdbsum/3ubt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubt ProSAT]</span></td></tr>
-<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=3ubt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubt OCA], [http://pdbe.org/3ubt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ubt RCSB], [http://www.ebi.ac.uk/pdbsum/3ubt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MTH3_HAEAE MTH3_HAEAE]] This methylase recognizes the double-stranded sequence GGCC, causes specific methylation on C-3 on both strands, and protects the DNA from cleavage by the HaeIII endonuclease.
+[https://www.uniprot.org/uniprot/MTH3_HAEAE MTH3_HAEAE] This methylase recognizes the double-stranded sequence GGCC, causes specific methylation on C-3 on both strands, and protects the DNA from cleavage by the HaeIII endonuclease.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Epigenetic methylation of cytosine residues in DNA is an essential element of genome maintenance and function in organisms ranging from bacteria to humans. DNA 5-cytosine methyltransferase enzymes (DCMTases) catalyze cytosine methylation via reaction intermediates in which the DNA is drastically remodeled, with the target cytosine residue extruded from the DNA helix and plunged into the active site pocket of the enzyme. We have determined a crystal structure of M.HaeIII DCMTase in complex with its DNA substrate at a previously unobserved state, prior to extrusion of the target cytosine and frameshifting of the DNA recognition sequence. The structure reveals that M.HaeIII selects the target cytosine and destabilizes its base-pairing through a precise, focused, and coordinated assault on the duplex DNA, which isolates the target cytosine from its nearest neighbors and thereby facilitates its extrusion from DNA.
-Structural origins of DNA target selection and nucleobase extrusion by a DNA Cytosine methyltransferase.,Didovyk A, Verdine GL J Biol Chem. 2012 Nov 23;287(48):40099-105. doi: 10.1074/jbc.M112.413054. Epub, 2012 Sep 25. PMID:23012373<ref>PMID:23012373</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3ubt" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus aegyptius trevisan 1889]]
+[[Category: Haemophilus aegyptius]]
-[[Category: Didovyk, A]]
+[[Category: Large Structures]]
-[[Category: Verdine, G L]]
+[[Category: Didovyk A]]
-[[Category: Cytosine-5 dna methylation]]
+[[Category: Verdine GL]]
-[[Category: Dna binding]]
-[[Category: Dna cytosine-5 methyltransferase]]
-[[Category: Protein-dna complex]]
-[[Category: S-adenosyl methionine binding]]
-[[Category: Transferase-dna complex]]