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3zde

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Current revision (07:12, 1 May 2024) (edit) (undo)
 
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<StructureSection load='3zde' size='340' side='right'caption='[[3zde]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
<StructureSection load='3zde' size='340' side='right'caption='[[3zde]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3zde]] is a 1 chain structure with sequence from [https://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=3ZDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZDE FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3zde]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZDE FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zd8|3zd8]], [[3zd9|3zd9]], [[3zda|3zda]], [[3zdb|3zdb]], [[3zdc|3zdc]], [[3zdd|3zdd]]</div></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]] 2.45&#8491;</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=3zde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zde OCA], [https://pdbe.org/3zde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zde RCSB], [https://www.ebi.ac.uk/pdbsum/3zde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zde 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=3zde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zde OCA], [https://pdbe.org/3zde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zde RCSB], [https://www.ebi.ac.uk/pdbsum/3zde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zde ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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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 3zde" 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: Bacillus coli migula 1895]]
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[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Anstey-Gilbert, C S]]
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[[Category: Anstey-Gilbert CS]]
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[[Category: Artymiuk, P J]]
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[[Category: Artymiuk PJ]]
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[[Category: Flemming, C S]]
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[[Category: Flemming CS]]
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[[Category: Hemsworth, G R]]
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[[Category: Hemsworth GR]]
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[[Category: Hodskinson, M R.G]]
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[[Category: Hodskinson MRG]]
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[[Category: Sayers, J R]]
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[[Category: Sayers JR]]
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[[Category: Sedelnikova, S E]]
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[[Category: Sedelnikova SE]]
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[[Category: Stillman, T J]]
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[[Category: Stillman TJ]]
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[[Category: Zhang, J]]
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[[Category: Zhang J]]
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[[Category: Dna binding]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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Current revision

Potassium free structure of E. coli ExoIX

PDB ID 3zde

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