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| | ==Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide== | | ==Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide== |
| - | <StructureSection load='4jrp' size='340' side='right' caption='[[4jrp]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='4jrp' size='340' side='right'caption='[[4jrp]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jrp]] is a 4 chain structure with sequence from [http://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=4JRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JRP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jrp]] 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=4JRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JRP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.95Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CY:1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM'>5CY</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CY:1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM'>5CY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jrq|4jrq]], [[4js4|4js4]], [[4js5|4js5]]</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=4jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jrp OCA], [https://pdbe.org/4jrp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jrp RCSB], [https://www.ebi.ac.uk/pdbsum/4jrp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jrp ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sbcB, cpeA, xonA, b2011, JW1993 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_I Exodeoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.1 3.1.11.1] </span></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=4jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jrp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jrp RCSB], [http://www.ebi.ac.uk/pdbsum/4jrp PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/EX1_ECOLI EX1_ECOLI] Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4jrp" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Exonuclease|Exonuclease]] | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli k-12]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Exodeoxyribonuclease I]] | + | [[Category: Large Structures]] |
| - | [[Category: Bell, C E]] | + | [[Category: Bell CE]] |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Dnaq superfamily]]
| + | |
| - | [[Category: Exonuclease]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| Structural highlights
4jrp is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.95Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
EX1_ECOLI Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase.
Publication Abstract from PubMed
Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3'-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an 'anchor' site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 A, reveals an Mg2+ ion bound to the scissile phosphate in a position corresponding to MgB in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed.
Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.,Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE Nucleic Acids Res. 2013 Apr 22. PMID:23609540[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE. Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion. Nucleic Acids Res. 2013 Apr 22. PMID:23609540 doi:10.1093/nar/gkt278
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