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3e40

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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+==
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<StructureSection load='3e40' size='340' side='right' caption='[[3e40]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='3e40' size='340' side='right'caption='[[3e40]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3e40]] 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=3E40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E40 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3e40]] 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=3E40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E40 FirstGlance]. <br>
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</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>
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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]] 2.1&#8491;</td></tr>
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<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>
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<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>
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<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>
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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=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>
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<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>
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<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=3e40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e40 RCSB], [http://www.ebi.ac.uk/pdbsum/3e40 PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[Endonuclease|Endonuclease]]
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Large Structures]]
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[[Category: Babic, A C]]
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[[Category: Babic AC]]
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[[Category: Horton, N C]]
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[[Category: Horton NC]]
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[[Category: Little, E J]]
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[[Category: Little EJ]]
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[[Category: Manohar, V M]]
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[[Category: Manohar VM]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Indirect readout]]
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[[Category: Nuclease]]
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[[Category: Protein-dna complex]]
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[[Category: Restriction system]]
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Current revision

Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+

PDB ID 3e40

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