2gb7: Difference between revisions

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 <StructureSection load='2gb7' size='340' side='right'caption='[[2gb7]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gb7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GB7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gb7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GB7 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fqz|2fqz]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ecl18kIR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gb7 OCA], [https://pdbe.org/2gb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gb7 RCSB], [https://www.ebi.ac.uk/pdbsum/2gb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gb7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O87963_ENTCL O87963_ENTCL]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gb7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.
-Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.,Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V EMBO J. 2006 May 17;25(10):2219-29. Epub 2006 Apr 20. PMID:16628220<ref>PMID:16628220</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2gb7" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Endonuclease 3D structures|Endonuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Enterobacter cloacae]]
 [[Category: Large Structures]]
-[[Category: Bochtler, M]]
+[[Category: Bochtler M]]
-[[Category: Czapinska, H]]
+[[Category: Czapinska H]]
-[[Category: Grazulis, S]]
+[[Category: Grazulis S]]
-[[Category: Manakova, E]]
+[[Category: Manakova E]]
-[[Category: Siksnys, V]]
+[[Category: Siksnys V]]
-[[Category: Szczepanowski, R H]]
+[[Category: Szczepanowski RH]]
-[[Category: Tamulaitis, G]]
+[[Category: Tamulaitis G]]
-[[Category: Base extrusion]]
-[[Category: Ecl18ki-dna complex]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Nucleotide flipping]]
-[[Category: Type ii restriction endonuclease]]