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| | <StructureSection load='4unf' size='340' side='right'caption='[[4unf]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='4unf' size='340' side='right'caption='[[4unf]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4unf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UNF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4unf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UNF 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uob|4uob]]</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=4unf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4unf OCA], [https://pdbe.org/4unf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4unf RCSB], [https://www.ebi.ac.uk/pdbsum/4unf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4unf ProSAT]</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=4unf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4unf OCA], [http://pdbe.org/4unf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4unf RCSB], [http://www.ebi.ac.uk/pdbsum/4unf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4unf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q9RRQ0_DEIRA Q9RRQ0_DEIRA]] DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435] | + | [https://www.uniprot.org/uniprot/Q9RRQ0_DEIRA Q9RRQ0_DEIRA] DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Endonuclease|Endonuclease]] | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deira]] | + | [[Category: Deinococcus radiodurans R1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hall, D]] | + | [[Category: Hall D]] |
| - | [[Category: Klar, T]] | + | [[Category: Klar T]] |
| - | [[Category: McSweeney, S]] | + | [[Category: McSweeney S]] |
| - | [[Category: Moe, E]] | + | [[Category: Moe E]] |
| - | [[Category: Okvist, M]] | + | [[Category: Okvist M]] |
| - | [[Category: Sarre, A]] | + | [[Category: Sarre A]] |
| - | [[Category: Smalas, A O]] | + | [[Category: Smalas AO]] |
| - | [[Category: Timmins, J]] | + | [[Category: Timmins J]] |
| - | [[Category: Base excision repair]]
| + | |
| - | [[Category: Dna glycosylase]]
| + | |
| - | [[Category: Fes cluster]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
Q9RRQ0_DEIRA DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435]
Publication Abstract from PubMed
While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Delta76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all alpha-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity.
Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.,Sarre A, Okvist M, Klar T, Hall DR, Smalas AO, McSweeney S, Timmins J, Moe E J Struct Biol. 2015 Jul 11. pii: S1047-8477(15)00138-0. doi:, 10.1016/j.jsb.2015.05.009. PMID:26172070[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sarre A, Okvist M, Klar T, Hall DR, Smalas AO, McSweeney S, Timmins J, Moe E. Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans. J Struct Biol. 2015 Jul 11. pii: S1047-8477(15)00138-0. doi:, 10.1016/j.jsb.2015.05.009. PMID:26172070 doi:http://dx.doi.org/10.1016/j.jsb.2015.05.009
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