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| | <StructureSection load='2ibt' size='340' side='right'caption='[[2ibt]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2ibt' size='340' side='right'caption='[[2ibt]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ibt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IBT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ibt]] is a 6 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=2IBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IBT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NEA:5-DEOXY-5-[2-(AMINO)ETHYLTHIO]ADENOSINE'>NEA</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]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene>, <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=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene>, <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 id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1g38|1g38]], [[2adm|2adm]], [[1aqi|1aqi]], [[1aqj|1aqj]], [[2ibs|2ibs]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">taqIM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </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=2ibt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ibt OCA], [https://pdbe.org/2ibt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ibt RCSB], [https://www.ebi.ac.uk/pdbsum/2ibt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ibt ProSAT]</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=2ibt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ibt OCA], [https://pdbe.org/2ibt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ibt RCSB], [https://www.ebi.ac.uk/pdbsum/2ibt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ibt ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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.
| + | [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. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 25104]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lenz, T]] | + | [[Category: Thermus aquaticus]] |
| - | [[Category: Scheidig, A J]] | + | [[Category: Lenz T]] |
| - | [[Category: Weinhold, E]] | + | [[Category: Scheidig AJ]] |
| - | [[Category: 2-aminopurine]] | + | [[Category: Weinhold E]] |
| - | [[Category: Abasic site analog]]
| + | |
| - | [[Category: Base flipping]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Dna methyltransferase]]
| + | |
| - | [[Category: Nucleotide flipping]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
2ibt is a 6 chain structure with sequence from Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.7Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.
2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence.,Lenz T, Bonnist EY, Pljevaljcic G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E J Am Chem Soc. 2007 May 16;129(19):6240-8. Epub 2007 Apr 25. PMID:17455934[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lenz T, Bonnist EY, Pljevaljcic G, Neely RK, Dryden DT, Scheidig AJ, Jones AC, Weinhold E. 2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence. J Am Chem Soc. 2007 May 16;129(19):6240-8. Epub 2007 Apr 25. PMID:17455934 doi:http://dx.doi.org/10.1021/ja069366n
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