6eko
From Proteopedia
(Difference between revisions)
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==Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA== | ==Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA== | ||
| - | <StructureSection load='6eko' size='340' side='right' caption='[[6eko]], [[Resolution|resolution]] 2.28Å' scene=''> | + | <StructureSection load='6eko' size='340' side='right'caption='[[6eko]], [[Resolution|resolution]] 2.28Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6eko]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6eko]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKO 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></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=6eko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eko OCA], [http://pdbe.org/6eko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eko RCSB], [http://www.ebi.ac.uk/pdbsum/6eko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eko ProSAT]</span></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=6eko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eko OCA], [http://pdbe.org/6eko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eko RCSB], [http://www.ebi.ac.uk/pdbsum/6eko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eko ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Restriction endonucleases (REs) of the CCGG-family recognize a set of 4-8 bp target sequences that share a common CCGG or CCNGG core and possess PD...D/ExK nuclease fold. REs that interact with 5 bp sequence 5'-CCNGG flip the central N nucleotides and 'compress' the bound DNA to stack the inner base pairs to mimic the CCGG sequence. PfoI belongs to the CCGG-family and cleaves the 7 bp sequence 5'-T|CCNGGA ("|" designates cleavage position). We present here crystal structures of PfoI in free and DNA-bound forms that show unique active site arrangement and mechanism of sequence recognition. Structures and mutagenesis indicate that PfoI features a permuted E...ExD...K active site that differs from the consensus motif characteristic to other family members. Although PfoI also flips the central N nucleotides of the target sequence it does not 'compress' the bound DNA. Instead, PfoI induces a drastic change in DNA backbone conformation that shortens the distance between scissile phosphates to match that in the unperturbed CCGG sequence. Our data demonstrate the diversity and versatility of structural mechanisms employed by restriction enzymes for recognition of related DNA sequences. | ||
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| + | Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.,Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V Nucleic Acids Res. 2019 Jan 25;47(2):997-1010. doi: 10.1093/nar/gky1137. PMID:30445642<ref>PMID:30445642</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6eko" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus fluorescens liquefaciens flugge 1886]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
[[Category: Grazulis, S]] | [[Category: Grazulis, S]] | ||
Revision as of 07:51, 24 April 2019
Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA
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