3e3y: Difference between revisions

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 ==Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+==
-<StructureSection load='3e3y' size='340' side='right' caption='[[3e3y]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
+<StructureSection load='3e3y' size='340' side='right'caption='[[3e3y]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3e3y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E3Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3e3y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E3Y FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.13&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tx3|1tx3]], [[2gij|2gij]], [[3e40|3e40]], [[3e41|3e41]], [[3e42|3e42]], [[3e43|3e43]], [[3e44|3e44]], [[3e45|3e45]]</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=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</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=3e3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e3y OCA], [https://pdbe.org/3e3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e3y RCSB], [https://www.ebi.ac.uk/pdbsum/3e3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e3y ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=3e3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e3y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e3y RCSB], [http://www.ebi.ac.uk/pdbsum/3e3y PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
+[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.
-DNA distortion and specificity in a sequence-specific endonuclease.,Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC J Mol Biol. 2008 Oct 31;383(1):186-204. Epub 2008 Aug 22. PMID:18762194<ref>PMID:18762194</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Haemophilus influenzae]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Large Structures]]
-[[Category: Babic, A C]]
+[[Category: Babic AC]]
-[[Category: Horton, N C]]
+[[Category: Horton NC]]
-[[Category: Little, E J]]
+[[Category: Little EJ]]
-[[Category: Manohar, V M]]
+[[Category: Manohar VM]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Indirect readout]]
-[[Category: Nuclease]]
-[[Category: Protein-dna complex]]
-[[Category: Restriction system]]