View source for 3ndh


==Restriction endonuclease in complex with substrate DNA==
<StructureSection load='3ndh' size='340' side='right' caption='[[3ndh]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ndh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NDH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</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=3ndh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ndh OCA], [http://pdbe.org/3ndh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ndh RCSB], [http://www.ebi.ac.uk/pdbsum/3ndh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ndh ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 A resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.

DNA intercalation without flipping in the specific ThaI-DNA complex.,Firczuk M, Wojciechowski M, Czapinska H, Bochtler M Nucleic Acids Res. 2011 Jan 1;39(2):744-54. Epub 2010 Sep 21. PMID:20861000<ref>PMID:20861000</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ndh" style="background-color:#fffaf0;"></div>

==See Also==
*[[Endonuclease|Endonuclease]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bochtler, M]]
[[Category: Czapinska, H]]
[[Category: Firczuk, M]]
[[Category: Wojciechowski, M]]
[[Category: Endonuclease-dna complex]]
[[Category: Hydrolase-dna complex]]
[[Category: Intercalation]]
[[Category: Restriction enzyme]]
[[Category: Thai]]