3e40: Difference between revisions
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==Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+== | ==Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+== | ||
<StructureSection load='3e40' size='340' side='right' caption='[[3e40]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='3e40' size='340' side='right'caption='[[3e40]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3e40]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3e40]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E40 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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e3y|3e3y]], [[3e41|3e41]], [[3e42|3e42]], [[3e43|3e43]], [[3e44|3e44]], [[3e45|3e45]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e3y|3e3y]], [[3e41|3e41]], [[3e42|3e42]], [[3e43|3e43]], [[3e44|3e44]], [[3e45|3e45]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e40 OCA], [https://pdbe.org/3e40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e40 RCSB], [https://www.ebi.ac.uk/pdbsum/3e40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e40 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 23: | Line 23: | ||
==See Also== | ==See Also== | ||
*[[Endonuclease|Endonuclease]] | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 29: | Line 29: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacterium influenzae lehmann and neumann 1896]] | [[Category: Bacterium influenzae lehmann and neumann 1896]] | ||
[[Category: Large Structures]] | |||
[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
[[Category: Babic, A C]] | [[Category: Babic, A C]] | ||
Revision as of 22:34, 20 October 2021
Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+
Structural highlights
Function[T2D2_HAEIN] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3. Publication Abstract from PubMedFive 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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