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| - | [[Image:1tx3.gif|left|200px]] | |
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| - | <!-- | + | ==HINCII BOUND TO COGNATE DNA== |
| - | The line below this paragraph, containing "STRUCTURE_1tx3", creates the "Structure Box" on the page.
| + | <StructureSection load='1tx3' size='340' side='right'caption='[[1tx3]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <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> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | {{STRUCTURE_1tx3| PDB=1tx3 | SCENE= }}
| + | <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> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3. |
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| - | '''HINCII BOUND TO COGNATE DNA'''
| + | ==See Also== |
| - | | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | 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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| - | ==About this Structure==
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| - | 1TX3 is a [[Single protein]] structure of 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=1TX3 OCA].
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| - | ==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15491133 15491133]
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| | [[Category: Haemophilus influenzae]] | | [[Category: Haemophilus influenzae]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Type II site-specific deoxyribonuclease]]
| + | [[Category: Dorner LF]] |
| - | [[Category: Dorner, L F.]] | + | [[Category: Horton NC]] |
| - | [[Category: Horton, N C.]] | + | [[Category: Perona JJ]] |
| - | [[Category: Perona, J J.]] | + | |
| - | [[Category: Blunt cutting]]
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| - | [[Category: Dna bending]]
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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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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 10:28:34 2008''
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