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| | ==Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA== | | ==Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA== |
| - | <StructureSection load='4hqb' size='340' side='right' caption='[[4hqb]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='4hqb' size='340' side='right'caption='[[4hqb]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hqb]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hqb]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQB FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddrB, ddrB (DR0070), DR_0070 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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]] 2.301Å</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=4hqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqb OCA], [http://pdbe.org/4hqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hqb RCSB], [http://www.ebi.ac.uk/pdbsum/4hqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqb 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=4hqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqb OCA], [https://pdbe.org/4hqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqb RCSB], [https://www.ebi.ac.uk/pdbsum/4hqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DDRB_DEIRA DDRB_DEIRA]] ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Appears to play a role in DNA repair and genome reconstitution, in a RecA-independent process, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. Binds single-stranded DNA but not duplex DNA.<ref>PMID:15454524</ref> <ref>PMID:19515845</ref> | + | [https://www.uniprot.org/uniprot/DDRB_DEIRA DDRB_DEIRA] ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Appears to play a role in DNA repair and genome reconstitution, in a RecA-independent process, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. Binds single-stranded DNA but not duplex DNA.<ref>PMID:15454524</ref> <ref>PMID:19515845</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Micrococcus radiodurans raj et al. 1960]] | + | [[Category: Deinococcus radiodurans]] |
| - | [[Category: Junop, M S]] | + | [[Category: Large Structures]] |
| - | [[Category: Sugiman-Marangos, S N]] | + | [[Category: Junop MS]] |
| - | [[Category: Dna annealing]] | + | [[Category: Sugiman-Marangos SN]] |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| Structural highlights
Function
DDRB_DEIRA ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Appears to play a role in DNA repair and genome reconstitution, in a RecA-independent process, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. Binds single-stranded DNA but not duplex DNA.[1] [2]
Publication Abstract from PubMed
The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use of a protein, DdrB, shown to greatly stimulate ssDNA annealing. Here, we report the structure of DdrB bound to ssDNA to 2.3 A. Pentameric DdrB was found to assemble into higher-order structures that coat ssDNA. To gain further mechanistic insight into the protein's function, a number of point mutants were generated altering both DNA binding and higher order oligomerization. This work not only identifies higher-order DdrB associations but also suggests the presence of an extended DNA binding surface running along the 'top' surface of a DdrB pentamer and continuing down between two individual subunits of the ring structure. Together this work sheds new insight into possible mechanisms for DdrB function in which higher-order assemblies of DdrB pentamers assist in the pairing of complementary ssDNA using an extended DNA binding surface.
Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.,Sugiman-Marangos SN, Peel JK, Weiss YM, Ghirlando R, Junop MS Nucleic Acids Res. 2013 Aug 23. PMID:23975200[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics. 2004 Sep;168(1):21-33. PMID:15454524 doi:http://dx.doi.org/10.1534/genetics.104.029249
- ↑ Norais CA, Chitteni-Pattu S, Wood EA, Inman RB, Cox MM. DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. J Biol Chem. 2009 Aug 7;284(32):21402-11. doi: 10.1074/jbc.M109.010454. Epub 2009, Jun 10. PMID:19515845 doi:http://dx.doi.org/10.1074/jbc.M109.010454
- ↑ Sugiman-Marangos SN, Peel JK, Weiss YM, Ghirlando R, Junop MS. Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states. Nucleic Acids Res. 2013 Aug 23. PMID:23975200 doi:10.1093/nar/gkt759
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