4dnb

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[[Image:4dnb.jpg|left|200px]]
 
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==METHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONFORMATION. THE CRYSTAL STRUCTURE OF D(CGCGAM6ATTCGCG) AT 2.0 ANGSTROMS RESOLUTION==
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The line below this paragraph, containing "STRUCTURE_4dnb", creates the "Structure Box" on the page.
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<StructureSection load='4dnb' size='340' side='right'caption='[[4dnb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[4dnb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DNB FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
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{{STRUCTURE_4dnb| PDB=4dnb | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dnb OCA], [https://pdbe.org/4dnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dnb RCSB], [https://www.ebi.ac.uk/pdbsum/4dnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dnb ProSAT]</span></td></tr>
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</table>
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'''METHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONFORMATION. THE CRYSTAL STRUCTURE OF D(CGCGAM6ATTCGCG) AT 2.0 ANGSTROMS RESOLUTION'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Frederick CA]]
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Methylation of nucleic acid bases is known to prevent the cleavage of DNA by restriction endonucleases. The effect on the conformation of the DNA molecule itself and hence its interactions with other DNA binding proteins has been a subject of general interest. To help address this question, we have solved the crystal structure at 2.0 A of the methylated dodecamer, d(CGCGAm6ATTCGCG), which contains the EcoRI recognition sequence and have compared the conformation of the methylated molecule with that of its nonmethylated counterpart. This methylation produces a bulky hydrophobic patch on the floor of the major groove of B-DNA which plays an important role in the mechanism of inhibition of EcoRI restriction activity. However, with the exception of small perturbations in the immediate vicinity of the methyl groups, the structure is virtually unchanged. Given the lack of a conformational change upon methylation, we have extended this thesis of the recognition process to other types of restriction systems and found that different restriction enzymes seem to have their own characteristic protein-DNA interactions. The relative spatial orientations of methylation sites and cleavage sites must play a major role in ordering protein secondary structure elements as well as subunit-subunit interactions along the DNA strand.
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[[Category: Quigley GJ]]
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[[Category: Rich A]]
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==About this Structure==
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[[Category: Van Boom JH]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNB OCA].
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[[Category: Van Der Marel GA]]
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[[Category: Wang AH-J]]
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==Reference==
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Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution., Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, Rich A, J Biol Chem. 1988 Nov 25;263(33):17872-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2846582 2846582]
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[[Category: Boom, J H.Van.]]
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[[Category: Frederick, C A.]]
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[[Category: Marel, G A.Van Der.]]
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[[Category: Quigley, G J.]]
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[[Category: Rich, A.]]
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[[Category: Wang, A H.J.]]
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[[Category: B-dna]]
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[[Category: Double helix]]
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[[Category: Modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:23:08 2008''
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Current revision

METHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONFORMATION. THE CRYSTAL STRUCTURE OF D(CGCGAM6ATTCGCG) AT 2.0 ANGSTROMS RESOLUTION

PDB ID 4dnb

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