2dvy

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==Crystal structure of restriction endonucleases PabI==
==Crystal structure of restriction endonucleases PabI==
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<StructureSection load='2dvy' size='340' side='right' caption='[[2dvy]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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<StructureSection load='2dvy' size='340' side='right'caption='[[2dvy]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2dvy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DVY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2dvy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVY FirstGlance]. <br>
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</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=2dvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dvy RCSB], [http://www.ebi.ac.uk/pdbsum/2dvy PDBsum]</span></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]] 3&#8491;</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=2dvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvy OCA], [https://pdbe.org/2dvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvy RCSB], [https://www.ebi.ac.uk/pdbsum/2dvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvy ProSAT]</span></td></tr>
</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/Q9V2B6_PYRAB Q9V2B6_PYRAB]
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Although structures of many DNA-binding proteins have been solved, they fall into a limited number of folds. Here, we describe an approach that led to the finding of a novel DNA-binding fold. Based on the behavior of Type II restriction-modification gene complexes as mobile elements, our earlier work identified a restriction enzyme, R.PabI, and its cognate modification enzyme in Pyrococcus abyssi through comparison of closely related genomes. While the modification methyltransferase was easily recognized, R.PabI was predicted to have a novel 3D structure. We expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation system and determined its crystal structure. R.PabI turned out to adopt a novel protein fold. Homodimeric R.PabI has a curved anti-parallel beta-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding analyses have assigned it as the double-strand DNA-binding site. Unlike most restriction enzymes analyzed, R.PabI is able to cleave DNA in the absence of Mg(2+). These results demonstrate the value of genome comparison and the wheat-germ-based system in finding a novel DNA-binding motif in mobile DNases and, in general, a novel protein fold in horizontally transferred genes.
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Novel protein fold discovered in the PabI family of restriction enzymes.,Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I Nucleic Acids Res. 2007;35(6):1908-18. Epub 2007 Mar 1. PMID:17332011<ref>PMID:17332011</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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==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: Large Structures]]
[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
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[[Category: Endo, Y]]
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[[Category: Endo Y]]
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[[Category: Kamo, M]]
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[[Category: Kamo M]]
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[[Category: Kobayashi, I]]
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[[Category: Kobayashi I]]
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[[Category: Miyazono, K]]
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[[Category: Miyazono K]]
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[[Category: Nagata, K]]
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[[Category: Nagata K]]
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[[Category: Sawasaki, T]]
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[[Category: Sawasaki T]]
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[[Category: Tanokura, M]]
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[[Category: Tanokura M]]
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[[Category: Watanabe, M]]
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[[Category: Watanabe M]]
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[[Category: Hydrolase]]
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[[Category: Restriction endonuclease]]
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Current revision

Crystal structure of restriction endonucleases PabI

PDB ID 2dvy

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