|
|
| (2 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
|
| |
|
| ==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)== | | ==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)== |
| <StructureSection load='3e42' size='340' side='right' caption='[[3e42]], [[Resolution|resolution]] 2.68Å' scene=''> | | <StructureSection load='3e42' size='340' side='right'caption='[[3e42]], [[Resolution|resolution]] 2.68Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [http://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=3E42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E42 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3e42]] 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=3E42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E42 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]] 2.68Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e41|3e41]], [[2gih|2gih]], [[3e3y|3e3y]], [[3e40|3e40]], [[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 "Bacterium influenzae" Lehmann and Neumann 1896])</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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [https://pdbe.org/3e42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [https://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://pdbe.org/3e42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 3e42" style="background-color:#fffaf0;"></div>
| |
|
| |
|
| ==See Also== | | ==See Also== |
| *[[Endonuclease|Endonuclease]] | | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Bacterium influenzae lehmann and neumann 1896]] | | [[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 interaction]]
| |
| [[Category: Restriction endonuclease]]
| |
| [[Category: Restriction system]]
| |