3ldy: Difference between revisions
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==An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI== | |||
<StructureSection load='3ldy' size='340' side='right' caption='[[3ldy]], [[Resolution|resolution]] 1.97Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ldy]] is a 3 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LDY 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=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3m7k|3m7k]]</td></tr> | |||
<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 Pseudomonas alcaligenes])</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=3ldy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ldy RCSB], [http://www.ebi.ac.uk/pdbsum/3ldy PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Endonuclease|Endonuclease]] | *[[Endonuclease|Endonuclease]] | ||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Pseudomonas alcaligenes]] | [[Category: Pseudomonas alcaligenes]] | ||
[[Category: Chan, S H | [[Category: Chan, S H]] | ||
[[Category: Heiter, D | [[Category: Heiter, D]] | ||
[[Category: Shen, B W | [[Category: Shen, B W]] | ||
[[Category: Stoddard, B L | [[Category: Stoddard, B L]] | ||
[[Category: Wilson, G | [[Category: Wilson, G]] | ||
[[Category: Xu, S Y | [[Category: Xu, S Y]] | ||
[[Category: A-a]] | [[Category: A-a]] | ||
[[Category: And t-t base-pair]] | [[Category: And t-t base-pair]] | ||
