3zdb: Difference between revisions

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 ==Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, di-magnesium and potassium==
-<StructureSection load='3zdb' size='340' side='right' caption='[[3zdb]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
+<StructureSection load='3zdb' size='340' side='right'caption='[[3zdb]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zdb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZDB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zdb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZDB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 1.47&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3zd8|3zd8]], [[3zd9|3zd9]], [[3zda|3zda]], [[3zdc|3zdc]], [[3zdd|3zdd]], [[3zde|3zde]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3zdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zdb OCA], [http://pdbe.org/3zdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zdb RCSB], [http://www.ebi.ac.uk/pdbsum/3zdb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zdb ProSAT]</span></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=3zdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zdb OCA], [https://pdbe.org/3zdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zdb RCSB], [https://www.ebi.ac.uk/pdbsum/3zdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zdb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/XNI_ECO57 XNI_ECO57]] May have a role in processing of nucleic acids. It is probably not an exonuclease; metal-binding residues found in paralogs are missing (By similarity).
+[https://www.uniprot.org/uniprot/XNI_ECO57 XNI_ECO57] May have a role in processing of nucleic acids. It is probably not an exonuclease; metal-binding residues found in paralogs are missing (By similarity).
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Escherichia coli Exonuclease IX (ExoIX), encoded by the xni gene, was the first identified member of a novel subfamily of ubiquitous flap endonucleases (FENs), which possess only one of the two catalytic metal-binding sites characteristic of other FENs. We have solved the first structure of one of these enzymes, that of ExoIX itself, at high resolution in DNA-bound and DNA-free forms. In the enzyme-DNA cocrystal, the single catalytic site binds two magnesium ions. The structures also reveal a binding site in the C-terminal domain where a potassium ion is directly coordinated by five main chain carbonyl groups, and we show this site is essential for DNA binding. This site resembles structurally and functionally the potassium sites in the human FEN1 and exonuclease 1 enzymes. Fluorescence anisotropy measurements and the crystal structures of the ExoIX:DNA complexes show that this potassium ion interacts directly with a phosphate diester in the substrate DNA.
-The structure of Escherichia coli ExoIX--implications for DNA binding and catalysis in flap endonucleases.,Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MR, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ Nucleic Acids Res. 2013 Jul 2. PMID:23821668<ref>PMID:23821668</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3zdb" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Anstey-Gilbert, C S]]
+[[Category: Large Structures]]
-[[Category: Artymiuk, P J]]
+[[Category: Synthetic construct]]
-[[Category: Flemming, C S]]
+[[Category: Anstey-Gilbert CS]]
-[[Category: Hemsworth, G R]]
+[[Category: Artymiuk PJ]]
-[[Category: Hodskinson, M R.G]]
+[[Category: Flemming CS]]
-[[Category: Sayers, J R]]
+[[Category: Hemsworth GR]]
-[[Category: Sedelnikova, S E]]
+[[Category: Hodskinson MRG]]
-[[Category: Stillman, T J]]
+[[Category: Sayers JR]]
-[[Category: Zhang, J]]
+[[Category: Sedelnikova SE]]
-[[Category: Dna binding]]
+[[Category: Stillman TJ]]
-[[Category: Flap endonuclease]]
+[[Category: Zhang J]]
-[[Category: Hydrolase-dna complex]]