2gb7

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[[Image:2gb7.gif|left|200px]]
 
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{{Structure
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==Metal-depleted Ecl18kI in complex with uncleaved, modified DNA==
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|PDB= 2gb7 |SIZE=350|CAPTION= <scene name='initialview01'>2gb7</scene>, resolution 1.7&Aring;
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<StructureSection load='2gb7' size='340' side='right'caption='[[2gb7]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<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>
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|ACTIVITY=
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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]] 1.7&#8491;</td></tr>
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|GENE= ecl18kIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 Enterobacter cloacae])
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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=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>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2fqz|2FQZ]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gb7 OCA], [http://www.ebi.ac.uk/pdbsum/2gb7 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2gb7 RCSB]</span>
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[https://www.uniprot.org/uniprot/O87963_ENTCL O87963_ENTCL]
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gb/2gb7_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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'''Metal-depleted Ecl18kI in complex with uncleaved, modified DNA'''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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==About this Structure==
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2GB7 is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16628220 16628220]
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[[Category: Enterobacter cloacae]]
[[Category: Enterobacter cloacae]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bochtler, M.]]
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[[Category: Bochtler M]]
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[[Category: Czapinska, H.]]
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[[Category: Czapinska H]]
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[[Category: Grazulis, S.]]
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[[Category: Grazulis S]]
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[[Category: Manakova, E.]]
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[[Category: Manakova E]]
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[[Category: Siksnys, V.]]
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[[Category: Siksnys V]]
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[[Category: Szczepanowski, R H.]]
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[[Category: Szczepanowski RH]]
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[[Category: Tamulaitis, G.]]
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[[Category: Tamulaitis G]]
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[[Category: base extrusion]]
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[[Category: ecl18ki-dna complex]]
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[[Category: nucleotide flipping]]
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[[Category: type ii restriction endonuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:14:19 2008''
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Current revision

Metal-depleted Ecl18kI in complex with uncleaved, modified DNA

PDB ID 2gb7

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