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| | ==Crystal Structure of Borrelia burgdorferi Pur-alpha== | | ==Crystal Structure of Borrelia burgdorferi Pur-alpha== |
| - | <StructureSection load='3n8b' size='340' side='right' caption='[[3n8b]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3n8b' size='340' side='right'caption='[[3n8b]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n8b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35210 Atcc 35210]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N8B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n8b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Borreliella_burgdorferi Borreliella burgdorferi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N8B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k44|3k44]]</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=3n8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n8b OCA], [https://pdbe.org/3n8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n8b RCSB], [https://www.ebi.ac.uk/pdbsum/3n8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n8b ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BB_0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=139 ATCC 35210])</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=3n8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n8b OCA], [http://pdbe.org/3n8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n8b RCSB], [http://www.ebi.ac.uk/pdbsum/3n8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n8b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/BPUR_BORBU BPUR_BORBU] A transcription and translation regulator. Binds DNA adjacent to the erp transcriptional promoter; in combination with BpbA inhibits transcription from the promoter (PubMed:23846702). EbfC counteracts the effect of Bpur on BpbA (PubMed:23846702). Overexpression leads to decreased amounts of ErpA protein (PubMed:23846702). Binds DNA and RNA; binds preferentially to RNA (dissociation constant 13 nM), dsDNA (dissociation constant 130 nM) and least well to ssDNA (dissociation constant 390 nM) (PubMed:23846702). Binds to its own (RNA) transcript in vivo and in vitro but not to its (DNA) promoter; inhibits translation from its mRNA (PubMed:23974034). Binds mRNA for superoxide dismutase (sod, SodA) but not the sod promoter; increased expression of BpuR leads to decreased levels of SodA (PubMed:31240776). May post-translationally influence the levels of other proteins also (Probable) (PubMed:31240776). Prefers purine-rich over pyrimidine-rich nucleic acids (PubMed:23846702, PubMed:20976240). Separates the strands of dsDNA (PubMed:23846702).<ref>PMID:20976240</ref> <ref>PMID:23846702</ref> <ref>PMID:31240776</ref> <ref>PMID:31240776</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n8/3n8b_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n8/3n8b_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 35210]] | + | [[Category: Borreliella burgdorferi]] |
| - | [[Category: Graebsch, A]] | + | [[Category: Large Structures]] |
| - | [[Category: Kostrewa, D]] | + | [[Category: Graebsch A]] |
| - | [[Category: Niessing, D]] | + | [[Category: Kostrewa D]] |
| - | [[Category: Roche, S]] | + | [[Category: Niessing D]] |
| - | [[Category: Dna binding]]
| + | [[Category: Roche S]] |
| - | [[Category: Nucleic acid binding protein]]
| + | |
| - | [[Category: Pur domain]]
| + | |
| - | [[Category: Pur repeat]]
| + | |
| - | [[Category: Pur-alpha]]
| + | |
| - | [[Category: Rna binding]]
| + | |
| - | [[Category: Whirly fold]]
| + | |
| Structural highlights
Function
BPUR_BORBU A transcription and translation regulator. Binds DNA adjacent to the erp transcriptional promoter; in combination with BpbA inhibits transcription from the promoter (PubMed:23846702). EbfC counteracts the effect of Bpur on BpbA (PubMed:23846702). Overexpression leads to decreased amounts of ErpA protein (PubMed:23846702). Binds DNA and RNA; binds preferentially to RNA (dissociation constant 13 nM), dsDNA (dissociation constant 130 nM) and least well to ssDNA (dissociation constant 390 nM) (PubMed:23846702). Binds to its own (RNA) transcript in vivo and in vitro but not to its (DNA) promoter; inhibits translation from its mRNA (PubMed:23974034). Binds mRNA for superoxide dismutase (sod, SodA) but not the sod promoter; increased expression of BpuR leads to decreased levels of SodA (PubMed:31240776). May post-translationally influence the levels of other proteins also (Probable) (PubMed:31240776). Prefers purine-rich over pyrimidine-rich nucleic acids (PubMed:23846702, PubMed:20976240). Separates the strands of dsDNA (PubMed:23846702).[1] [2] [3] [4]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Pur-alpha is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-alpha was possible. However, recently we solved the X-ray structure of Pur-alpha from the fruitfly Drosophila melanogaster and showed that it contains a so-called PUR domain. Here we explain how we exploited bioinformatics tools in combination with X-ray structure determination of a bacterial homolog to obtain diffracting crystals and the high-resolution structure of Drosophila Pur-alpha. First, we used sensitive methods for remote-homology detection to find three repetitive regions in Pur-alpha. We realized that our lack of understanding how these repeats interact to form a globular domain was a major problem for crystallization and structure determination. With our information on the repeat motifs we then identified a distant bacterial homolog that contains only one repeat. We determined the bacterial crystal structure and found that two of the repeats interact to form a globular domain. Based on this bacterial structure, we calculated a computational model of the eukaryotic protein. The model allowed us to design a crystallizable fragment and to determine the structure of Drosophila Pur-alpha. Key for success was the fact that single repeats of the bacterial protein self-assembled into a globular domain, instructing us on the number and boundaries of repeats to be included for crystallization trials with the eukaryotic protein. This study demonstrates that the simpler structural domain arrangement of a distant prokaryotic protein can guide the design of eukaryotic crystallization constructs. Since many eukaryotic proteins contain multiple repeats or repeating domains, this approach might be instructive for structural studies of a range of proteins.
Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.,Graebsch A, Roche S, Kostrewa D, Soding J, Niessing D PLoS One. 2010 Oct 14;5(10):e13402. doi: 10.1371/journal.pone.0013402. PMID:20976240[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Graebsch A, Roche S, Kostrewa D, Soding J, Niessing D. Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PLoS One. 2010 Oct 14;5(10):e13402. doi: 10.1371/journal.pone.0013402. PMID:20976240 doi:10.1371/journal.pone.0013402
- ↑ Jutras BL, Chenail AM, Carroll DW, Miller MC, Zhu H, Bowman A, Stevenson B. Bpur, the Lyme disease spirochete's PUR domain protein: identification as a transcriptional modulator and characterization of nucleic acid interactions. J Biol Chem. 2013 Sep 6;288(36):26220-26234. PMID:23846702 doi:10.1074/jbc.M113.491357
- ↑ Jutras BL, Savage CR, Arnold WK, Lethbridge KG, Carroll DW, Tilly K, Bestor A, Zhu H, Seshu J, Zückert WR, Stewart PE, Rosa PA, Brissette CA, Stevenson B. The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase. Mol Microbiol. 2019 Sep;112(3):973-991. PMID:31240776 doi:10.1111/mmi.14336
- ↑ Jutras BL, Savage CR, Arnold WK, Lethbridge KG, Carroll DW, Tilly K, Bestor A, Zhu H, Seshu J, Zückert WR, Stewart PE, Rosa PA, Brissette CA, Stevenson B. The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase. Mol Microbiol. 2019 Sep;112(3):973-991. PMID:31240776 doi:10.1111/mmi.14336
- ↑ Graebsch A, Roche S, Kostrewa D, Soding J, Niessing D. Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PLoS One. 2010 Oct 14;5(10):e13402. doi: 10.1371/journal.pone.0013402. PMID:20976240 doi:10.1371/journal.pone.0013402
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