1dfm: Difference between revisions

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-[[Image:1dfm.png|left|200px]]
-{{STRUCTURE_1dfm|  PDB=1dfm  |  SCENE=  }}
+==Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer==
+<StructureSection load='1dfm' size='340' side='right'caption='[[1dfm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dfm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1dfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfm OCA], [https://pdbe.org/1dfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dfm RCSB], [https://www.ebi.ac.uk/pdbsum/1dfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dfm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/T2B2_BACIU T2B2_BACIU] Recognizes the double-stranded sequence AGATCT and cleaves after A-1.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core, but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to provide extra specificity. Remarkably, the DNA is contorted differently in the two structures, leading to different protein-DNA contacts for even the common base pairs. Furthermore, the BglII active site contains a glutamine in place of the glutamate at the general base position in BamHI, and only a single metal is found coordinated to the putative nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows that different strategies can be successful in achieving site-specific recognition and catalysis in restriction endonucleases.
-===Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer===
+Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution.,Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK Nat Struct Biol. 2000 Feb;7(2):134-40. PMID:10655616<ref>PMID:10655616</ref>
-{{ABSTRACT_PUBMED_10655616}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1dfm" style="background-color:#fffaf0;"></div>
-[[1dfm]] is a 4 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFM OCA].
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010655616</ref><ref group="xtra">PMID:011742118</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Aggarwal, A K.]]
+[[Category: Large Structures]]
-[[Category: Kucera, R.]]
+[[Category: Aggarwal AK]]
-[[Category: Lukacs, C M.]]
+[[Category: Kucera R]]
-[[Category: Schildkraut, I.]]
+[[Category: Lukacs CM]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Schildkraut I]]
-[[Category: Protein-dna complex]]
-[[Category: Restriction endonuclease]]
-[[Category: Restriction enzyme]]