2ih5: Difference between revisions

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 ==Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target base partner position==
-<StructureSection load='2ih5' size='340' side='right' caption='[[2ih5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2ih5' size='340' side='right'caption='[[2ih5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ih5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IH5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ih5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IH5 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NEA:5-DEOXY-5-[2-(AMINO)ETHYLTHIO]ADENOSINE'>NEA</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NEA:5-DEOXY-5-[2-(AMINO)ETHYLTHIO]ADENOSINE'>NEA</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g38|1g38]], [[2adm|2adm]], [[1aqi|1aqi]], [[1aqj|1aqj]], [[2ibs|2ibs]], [[2ibt|2ibt]], [[2ih2|2ih2]], [[2ih4|2ih4]]</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=2ih5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ih5 OCA], [https://pdbe.org/2ih5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ih5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ih5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ih5 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">taqIM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </span></td></tr>
+== Function ==
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ih5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ih5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ih5 RCSB], [http://www.ebi.ac.uk/pdbsum/2ih5 PDBsum]</span></td></tr>
+[https://www.uniprot.org/uniprot/MTTA_THEAQ MTTA_THEAQ] This methylase recognizes the double-stranded sequence TCGA, causes specific methylation on A-4 on both strands and protects the DNA from cleavage by the TaqI endonuclease.
-<table>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/2ih5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/2ih5_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ih5 ConSurf].
 <div style="clear:both"></div>
 ==See Also==
-*[[DNA methyltransferase|DNA methyltransferase]]
+*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus aquaticus]]
-[[Category: Lenz, T.]]
+[[Category: Lenz T]]
-[[Category: Scheidig, A J.]]
+[[Category: Scheidig AJ]]
-[[Category: Weinhold, E.]]
+[[Category: Weinhold E]]
-[[Category: Abasic site analog]]
-[[Category: Base flipping]]
-[[Category: Dna]]
-[[Category: Dna methyltransferase]]
-[[Category: Nucleotide flipping]]
-[[Category: Target base partner]]
-[[Category: Transferase-dna complex]]