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| | ==HINCII BOUND TO COGNATE DNA== | | ==HINCII BOUND TO COGNATE DNA== |
| - | <StructureSection load='1tx3' size='340' side='right' caption='[[1tx3]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='1tx3' size='340' side='right'caption='[[1tx3]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1tx3]] is a 8 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=1TX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TX3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1tx3]] is a 8 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=1TX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TX3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.5Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1tx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tx3 OCA], [https://pdbe.org/1tx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tx3 RCSB], [https://www.ebi.ac.uk/pdbsum/1tx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tx3 ProSAT]</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=1tx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tx3 OCA], [http://pdbe.org/1tx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tx3 RCSB], [http://www.ebi.ac.uk/pdbsum/1tx3 PDBsum]</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;">
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| - | == Publication Abstract from PubMed ==
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| - | The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions.
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| - | Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.,Etzkorn C, Horton NC Biochemistry. 2004 Oct 26;43(42):13256-70. PMID:15491133<ref>PMID:15491133</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 1tx3" style="background-color:#fffaf0;"></div>
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| | ==See Also== | | ==See Also== |
| - | *[[Endonuclease|Endonuclease]] | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium influenzae lehmann and neumann 1896]] | + | [[Category: Haemophilus influenzae]] |
| - | [[Category: Type II site-specific deoxyribonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Dorner, L F]] | + | [[Category: Dorner LF]] |
| - | [[Category: Horton, N C]] | + | [[Category: Horton NC]] |
| - | [[Category: Perona, J J]] | + | [[Category: Perona JJ]] |
| - | [[Category: Blunt cutting]]
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| - | [[Category: Dna bending]]
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| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Indirect readout]]
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| - | [[Category: Protein-dna]]
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| - | [[Category: Restriction endonuclease]]
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