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5ffj

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==Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic==
==Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic==
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<StructureSection load='5ffj' size='340' side='right' caption='[[5ffj]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
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<StructureSection load='5ffj' size='340' side='right'caption='[[5ffj]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ffj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FFJ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ffj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FFJ FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xqk|4xqk]]</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]] 2.84&#8491;</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=5ffj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ffj OCA], [http://pdbe.org/5ffj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ffj RCSB], [http://www.ebi.ac.uk/pdbsum/5ffj PDBsum]</span></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=5ffj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ffj OCA], [https://pdbe.org/5ffj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ffj RCSB], [https://www.ebi.ac.uk/pdbsum/5ffj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ffj 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/Q93R01_9LACT Q93R01_9LACT]
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Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modification enzymes. We determined the structure of the Type ISP enzyme LlaGI bound to its target and compared it with the previously reported structure of a close homologue that binds to a distinct target, LlaBIII. The comparison revealed that, although the two enzymes use almost a similar set of structural elements for target recognition, the residues that read the bases vary. Change in specificity resulted not only from appropriate substitution of amino acids that contacted the bases but also from new contacts made by positionally distinct residues directly or through a water bridge. Sequence analyses of 552 Type ISP enzymes showed that the structural elements involved in target recognition of LlaGI and LlaBIII were structurally well-conserved but sequentially less-conserved. In addition, the residue positions within these structural elements were under strong evolutionary constraint, highlighting the functional importance of these regions. The comparative study helped decipher a partial consensus code for target recognition by Type ISP enzymes.
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Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.,Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD, Saikrishnan K Nucleic Acids Res. 2016 Mar 14. pii: gkw154. PMID:26975655<ref>PMID:26975655</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 5ffj" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Kulkarni, M]]
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[[Category: Lactococcus lactis]]
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[[Category: Nirwan, N]]
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[[Category: Large Structures]]
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[[Category: Saikrishnan, K]]
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[[Category: Unidentified]]
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[[Category: Dna binding protein-dna complex]]
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[[Category: Kulkarni M]]
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[[Category: Dna-binding protein]]
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[[Category: Nirwan N]]
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[[Category: Helicase-like atpase]]
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[[Category: Saikrishnan K]]
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[[Category: Methyltransferase]]
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[[Category: Restriction-modification enzyme]]
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Current revision

Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic

PDB ID 5ffj

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