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| | ==Crystal structure of apo E. coli XylR== | | ==Crystal structure of apo E. coli XylR== |
| - | <StructureSection load='4fe4' size='340' side='right' caption='[[4fe4]], [[Resolution|resolution]] 3.45Å' scene=''> | + | <StructureSection load='4fe4' size='340' side='right'caption='[[4fe4]], [[Resolution|resolution]] 3.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fe4]] is a 3 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=4FE4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FE4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fe4]] is a 3 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=4FE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FE4 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylR, b3569, JW3541 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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]] 3.45Å</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=4fe4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe4 OCA], [http://pdbe.org/4fe4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fe4 RCSB], [http://www.ebi.ac.uk/pdbsum/4fe4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fe4 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=4fe4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe4 OCA], [https://pdbe.org/4fe4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fe4 RCSB], [https://www.ebi.ac.uk/pdbsum/4fe4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fe4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYLR_ECOLI XYLR_ECOLI]] Regulatory protein for the xylBAFGHR operon. | + | [https://www.uniprot.org/uniprot/XYLR_ECOLI XYLR_ECOLI] Regulatory protein for the xylBAFGHR operon. |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Escherichia coli can rapidly switch to the metabolism of l-arabinose and d-xylose in the absence of its preferred carbon source, glucose, in a process called carbon catabolite repression. Transcription of the genes required for l-arabinose and d-xylose consumption is regulated by the sugar-responsive transcription factors, AraC and XylR. E. coli represents a promising candidate for biofuel production through the metabolism of hemicellulose, which is composed of d-xylose and l-arabinose. Understanding the l-arabinose/d-xylose regulatory network is key for such biocatalyst development. Unlike AraC, which is a well-studied protein, little is known about XylR. To gain insight into XylR function, we performed biochemical and structural studies. XylR contains a C-terminal AraC-like domain. However, its N-terminal d-xylose-binding domain contains a periplasmic-binding protein (PBP) fold with structural homology to LacI/GalR transcription regulators. Like LacI/GalR proteins, the XylR PBP domain mediates dimerization. However, unlike LacI/GalR proteins, which dimerize in a parallel, side-to-side manner, XylR PBP dimers are antiparallel. Strikingly, d-xylose binding to this domain results in a helix to strand transition at the dimer interface that reorients both DNA-binding domains, allowing them to bind and loop distant operator sites. Thus, the combined data reveal the ligand-induced activation mechanism of a new family of DNA-binding proteins.
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| - | Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain.,Ni L, Tonthat NK, Chinnam N, Schumacher MA Nucleic Acids Res. 2012 Dec 14. PMID:23241389<ref>PMID:23241389</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4fe4" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ni, L]]
| + | [[Category: Large Structures]] |
| - | [[Category: Schumacher, M A]]
| + | [[Category: Ni L]] |
| - | [[Category: D-xylose]]
| + | [[Category: Schumacher MA]] |
| - | [[Category: Dauixie]] | + | |
| - | [[Category: Dna looping]] | + | |
| - | [[Category: Transcription]] | + | |
| - | [[Category: Xylr]]
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