4rtq: Difference between revisions
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==Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp non-canonical site (GTTTA )== | ==Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp non-canonical site (GTTTA )== | ||
<StructureSection load='4rtq' size='340' side='right' caption='[[4rtq]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='4rtq' size='340' side='right'caption='[[4rtq]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4rtq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTQ OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4rtq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MDS42 Escherichia coli str. K-12 substr. MDS42] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RTQ FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.997Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4rtq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtq OCA], [https://pdbe.org/4rtq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rtq RCSB], [https://www.ebi.ac.uk/pdbsum/4rtq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== 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. | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 15: | Line 18: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4rtq" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA adenine methylase|DNA adenine methylase]] | |||
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli str. K-12 substr. MDS42]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Cheng X]] | ||
[[Category: | [[Category: Horton JR]] | ||
Latest revision as of 20:55, 20 September 2023
Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp non-canonical site (GTTTA )Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp non-canonical site (GTTTA )
Structural highlights
FunctionDMA_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. Publication Abstract from PubMedDNA adenine methyltransferase (Dam) is widespread and conserved among the gamma-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.,Horton JR, Zhang X, Blumenthal RM, Cheng X Nucleic Acids Res. 2015 Apr 6. pii: gkv251. PMID:25845600[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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