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| | ==Exonuclease X in complex with 12bp blunt-ended dsDNA== | | ==Exonuclease X in complex with 12bp blunt-ended dsDNA== |
| - | <StructureSection load='4fzy' size='340' side='right' caption='[[4fzy]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='4fzy' size='340' side='right'caption='[[4fzy]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fzy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FZY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fzy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FZY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fzx|4fzx]], [[4fzz|4fzz]]</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=4fzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fzy OCA], [https://pdbe.org/4fzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fzy RCSB], [https://www.ebi.ac.uk/pdbsum/4fzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fzy ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">exoX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4fzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fzy OCA], [http://pdbe.org/4fzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fzy RCSB], [http://www.ebi.ac.uk/pdbsum/4fzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fzy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/EXOX_ECOLI EXOX_ECOLI]] Capable of degrading both single-strand and double-strand DNA with 3' to 5' polarity. Has higher affinity for ssDNA ends than for dsDNA. | + | [https://www.uniprot.org/uniprot/EXOX_ECOLI EXOX_ECOLI] Capable of degrading both single-strand and double-strand DNA with 3' to 5' polarity. Has higher affinity for ssDNA ends than for dsDNA. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4fzy" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4fzy" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Bi, L]] | + | [[Category: Large Structures]] |
| - | [[Category: Cheng, F]] | + | [[Category: Bi L]] |
| - | [[Category: Jiang, T]] | + | [[Category: Cheng F]] |
| - | [[Category: Sun, H]] | + | [[Category: Jiang T]] |
| - | [[Category: Wang, T]] | + | [[Category: Sun H]] |
| - | [[Category: Deddh]]
| + | [[Category: Wang T]] |
| - | [[Category: Dnaq family]]
| + | |
| - | [[Category: Exo]]
| + | |
| - | [[Category: Exonuclease]]
| + | |
| - | [[Category: Homologous recombination]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Mismatch repair]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Stabilization of tandem repeat]]
| + | |
| - | [[Category: Uv repair]]
| + | |
| Structural highlights
Function
EXOX_ECOLI Capable of degrading both single-strand and double-strand DNA with 3' to 5' polarity. Has higher affinity for ssDNA ends than for dsDNA.
Publication Abstract from PubMed
Members of the DnaQ superfamily are major 3'-5' exonucleases that degrade either only single-stranded DNA (ssDNA) or both ssDNA and double-stranded DNA (dsDNA). However, the mechanism by which dsDNA is recognized and digested remains unclear. Exonuclease X (ExoX) is a distributive DnaQ exonuclease that cleaves both ssDNA and dsDNA substrates. Here, we report the crystal structures of Escherichia coli ExoX in complex with three different dsDNA substrates: 3' overhanging dsDNA, blunt-ended dsDNA and 3' recessed mismatch-containing dsDNA. In these structures, ExoX binds to dsDNA via both a conserved substrate strand-interacting site and a previously uncharacterized complementary strand-interacting motif. When ExoX complexes with blunt-ended dsDNA or 5' overhanging dsDNA, a 'wedge' composed of Leu12 and Gln13 penetrates between the first two base pairs to break the 3' terminal base pair and facilitates precise feeding of the 3' terminus of the substrate strand into the ExoX cleavage active site. Site-directed mutagenesis showed that the complementary strand-binding site and the wedge of ExoX are dsDNA specific. Together with the results of structural comparisons, our data support a mechanism by which normal and mismatched dsDNA are recognized and digested by E. coli ExoX. The crystal structures also provide insight into the structural framework of the different substrate specificities of the DnaQ family members.
Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease.,Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T Nucleic Acids Res. 2013 Jun 14. PMID:23771145[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T. Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease. Nucleic Acids Res. 2013 Jun 14. PMID:23771145 doi:10.1093/nar/gkt495
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