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| | <StructureSection load='2g1p' size='340' side='right'caption='[[2g1p]], [[Resolution|resolution]] 1.89Å' scene=''> | | <StructureSection load='2g1p' size='340' side='right'caption='[[2g1p]], [[Resolution|resolution]] 1.89Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2g1p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G1P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2g1p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G1P 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=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]] 1.89Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fy3|1fy3]], [[1yfj|1yfj]], [[1yfl|1yfl]], [[1q0t|1q0t]], [[1q0s|1q0s]]</div></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=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dam ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2g1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g1p OCA], [https://pdbe.org/2g1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g1p RCSB], [https://www.ebi.ac.uk/pdbsum/2g1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g1p 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=2g1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g1p OCA], [https://pdbe.org/2g1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g1p RCSB], [https://www.ebi.ac.uk/pdbsum/2g1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g1p ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DMA_ECOLI DMA_ECOLI]] Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication.
| + | [https://www.uniprot.org/uniprot/DMA_ECOLI DMA_ECOLI] Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication. |
| | == 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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bekes, M]] | + | [[Category: Bekes M]] |
| - | [[Category: Cheng, X]] | + | [[Category: Cheng X]] |
| - | [[Category: Horton, J R]] | + | [[Category: Horton JR]] |
| - | [[Category: Jeltsch, A]] | + | [[Category: Jeltsch A]] |
| - | [[Category: Liebert, K]] | + | [[Category: Liebert K]] |
| - | [[Category: Bacterial virulence factor]]
| + | |
| - | [[Category: Base flipping]]
| + | |
| - | [[Category: Dam methylation]]
| + | |
| - | [[Category: Gatc recognition]]
| + | |
| - | [[Category: Transferase-dna complex]]
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| Structural highlights
Function
DMA_ECOLI Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication.
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
The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments. Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts to the non-target strand in the second (3') half of the GATC site are established by R124 to the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119 intercalates into the DNA between the second and third base-pairs, which is essential for base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam, three major new observations are made in E.coli Dam. (1) The first Gua is recognized by K9, removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds to the surface of EcoDam in the absence of S-adenosyl-L-methionine, which illustrates a possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays structural flexibility by adopting an extrahelical or intrahelical position where it is in contact to N120.
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.,Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X J Mol Biol. 2006 Apr 28;358(2):559-70. Epub 2006 Feb 28. PMID:16524590[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X. Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. J Mol Biol. 2006 Apr 28;358(2):559-70. Epub 2006 Feb 28. PMID:16524590 doi:10.1016/j.jmb.2006.02.028
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