3ldy

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==An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI==
==An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI==
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<StructureSection load='3ldy' size='340' side='right' caption='[[3ldy]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
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<StructureSection load='3ldy' size='340' side='right'caption='[[3ldy]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ldy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14909 Atcc 14909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LDY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ldy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_alcaligenes Pseudomonas alcaligenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LDY 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=ZN:ZINC+ION'>ZN</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]] 1.97&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3m7k|3m7k]]</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=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pacIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=43263 ATCC 14909])</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=3ldy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldy OCA], [https://pdbe.org/3ldy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ldy RCSB], [https://www.ebi.ac.uk/pdbsum/3ldy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldy ProSAT]</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=3ldy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldy OCA], [http://pdbe.org/3ldy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ldy RCSB], [http://www.ebi.ac.uk/pdbsum/3ldy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldy ProSAT]</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/D5MNX7_PSEAC D5MNX7_PSEAC]
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The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA base pairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures.
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Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.,Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL Structure. 2010 Jun 9;18(6):734-43. PMID:20541511<ref>PMID:20541511</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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<div class="pdbe-citations 3ldy" style="background-color:#fffaf0;"></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>
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[[Category: Atcc 14909]]
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[[Category: Large Structures]]
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[[Category: Chan, S H]]
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[[Category: Pseudomonas alcaligenes]]
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[[Category: Heiter, D]]
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[[Category: Chan S-H]]
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[[Category: Shen, B W]]
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[[Category: Heiter D]]
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[[Category: Stoddard, B L]]
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[[Category: Shen BW]]
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[[Category: Wilson, G]]
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[[Category: Stoddard BL]]
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[[Category: Xu, S Y]]
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[[Category: Wilson G]]
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[[Category: A-a]]
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[[Category: Xu S-Y]]
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[[Category: And t-t base-pair]]
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[[Category: Beta-beta-alpha-metal]]
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[[Category: Hnh motif]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Zinc cluster]]
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Current revision

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

PDB ID 3ldy

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