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| | ==DNA binding domain of restriction endonuclease bound to DNA== | | ==DNA binding domain of restriction endonuclease bound to DNA== |
| - | <StructureSection load='3ssc' size='340' side='right' caption='[[3ssc]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3ssc' size='340' side='right'caption='[[3ssc]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ssc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SSC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ssc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SSC FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ssd|3ssd]], [[3sse|3sse]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4346, JW5871, mcrB, rglB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3ssc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ssc OCA], [https://pdbe.org/3ssc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ssc RCSB], [https://www.ebi.ac.uk/pdbsum/3ssc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ssc 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=3ssc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ssc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ssc RCSB], [http://www.ebi.ac.uk/pdbsum/3ssc PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MCRB_ECOLI MCRB_ECOLI]] Recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue. Binds to DNA containing methylated cytosines; also binds to GTP. Isoform 33 kDa is less active than isoform 51 kDa and may play a role in regulating the activity of isoform 51 kDa by competing with it in DNA and protein binding abilities. | + | [https://www.uniprot.org/uniprot/MCRB_ECOLI MCRB_ECOLI] Recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue. Binds to DNA containing methylated cytosines; also binds to GTP. Isoform 33 kDa is less active than isoform 51 kDa and may play a role in regulating the activity of isoform 51 kDa by competing with it in DNA and protein binding abilities. |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | DNA cytosine methylation is a widespread epigenetic mark. Biological effects of DNA methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in different sequence contexts. Until now two different structural mechanisms have been established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination of the 5mC modification is achieved in prokaryotes. Here we report the crystal structure of the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from Escherichia coli. The McrB-N protein shows a novel DNA-binding fold adapted for 5mC-recognition. In the McrB-N structure in complex with methylated DNA, the 5mC base is flipped out from the DNA duplex and positioned within a binding pocket. Base flipping elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol., 64, 557-569]: flipped out 5-hydroxymethylcytosine is accommodated in the binding pocket but there is no room for the glycosylated base. The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds.
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| - | The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.,Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V Nucleic Acids Res. 2012 May 8. PMID:22570415<ref>PMID:22570415</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Grazulis, S]]
| + | [[Category: Large Structures]] |
| - | [[Category: Siksnys, V]]
| + | [[Category: Grazulis S]] |
| - | [[Category: Sukackaite, R]]
| + | [[Category: Siksnys V]] |
| - | [[Category: 5-methylcytosine]]
| + | [[Category: Sukackaite R]] |
| - | [[Category: Base flipping complex]] | + | |
| - | [[Category: Dna binding protein-dna complex]] | + | |
| - | [[Category: Protein-dna complex]] | + | |
| - | [[Category: Restriction endonuclease]] | + | |
