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| | <StructureSection load='2oxl' size='340' side='right'caption='[[2oxl]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='2oxl' size='340' side='right'caption='[[2oxl]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2oxl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2oxl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</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]] 1.8Å</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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ymgB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2oxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxl OCA], [https://pdbe.org/2oxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxl RCSB], [https://www.ebi.ac.uk/pdbsum/2oxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxl 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=2oxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxl OCA], [https://pdbe.org/2oxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxl RCSB], [https://www.ebi.ac.uk/pdbsum/2oxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxl ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ARIR_ECOLI ARIR_ECOLI]] Probably a connector protein for RcsB/C regulation of biofilm and acid-resistance, providing additional signal input into the two-component signaling pathway. May serve to stimulate biofilm maturation, via the Rcs phosphorelay. Regulates expression of genes involved in acid-resistance and biofilm formation, including the RcsB/C two-component system. May be a non-specific DNA-binding protein that binds genes and/or intergenic regions via a geometric recognition. Also confers resistance to H(2)O(2). Overexpression at 28 and 16 degrees Celsius increases the production of colanic acid, an exopolysaccharide and matrix component, and reduces adhesive curli fimbriae expression. Both of these effects require RcsB; AriR probably acts upstream of the RcsB/C system to stimulate the activity and not transcription of RcsB/C. 5-fluorouracil reduction in biofilm formation requires this protein.<ref>PMID:17765265</ref>
| + | [https://www.uniprot.org/uniprot/ARIR_ECOLI ARIR_ECOLI] Probably a connector protein for RcsB/C regulation of biofilm and acid-resistance, providing additional signal input into the two-component signaling pathway. May serve to stimulate biofilm maturation, via the Rcs phosphorelay. Regulates expression of genes involved in acid-resistance and biofilm formation, including the RcsB/C two-component system. May be a non-specific DNA-binding protein that binds genes and/or intergenic regions via a geometric recognition. Also confers resistance to H(2)O(2). Overexpression at 28 and 16 degrees Celsius increases the production of colanic acid, an exopolysaccharide and matrix component, and reduces adhesive curli fimbriae expression. Both of these effects require RcsB; AriR probably acts upstream of the RcsB/C system to stimulate the activity and not transcription of RcsB/C. 5-fluorouracil reduction in biofilm formation requires this protein.<ref>PMID:17765265</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/ox/2oxl_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ox/2oxl_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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Doshi, O]] | + | [[Category: Doshi O]] |
| - | [[Category: Page, R]] | + | [[Category: Page R]] |
| - | [[Category: Palermino, J M]] | + | [[Category: Palermino JM]] |
| - | [[Category: Peti, W]] | + | [[Category: Peti W]] |
| - | [[Category: Woods, T K]] | + | [[Category: Woods TK]] |
| - | [[Category: Acid resistance]]
| + | |
| - | [[Category: Bacterial protein]]
| + | |
| - | [[Category: Biofilm]]
| + | |
| - | [[Category: Dimer]]
| + | |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Gene regulation]]
| + | |
| Structural highlights
Function
ARIR_ECOLI Probably a connector protein for RcsB/C regulation of biofilm and acid-resistance, providing additional signal input into the two-component signaling pathway. May serve to stimulate biofilm maturation, via the Rcs phosphorelay. Regulates expression of genes involved in acid-resistance and biofilm formation, including the RcsB/C two-component system. May be a non-specific DNA-binding protein that binds genes and/or intergenic regions via a geometric recognition. Also confers resistance to H(2)O(2). Overexpression at 28 and 16 degrees Celsius increases the production of colanic acid, an exopolysaccharide and matrix component, and reduces adhesive curli fimbriae expression. Both of these effects require RcsB; AriR probably acts upstream of the RcsB/C system to stimulate the activity and not transcription of RcsB/C. 5-fluorouracil reduction in biofilm formation requires this protein.[1]
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
The Escherichia coli gene cluster ymgABC was identified in transcriptome studies to have a role in biofilm development and stability. In this study, we showed that YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility, and protects the cell from acid indicating that YmgB has a major role in acid-resistance in E. coli. Our data show that these phenotypes are potentially mediated through interactions with the important cell signal indole. In addition, gel mobility-shift assays suggest that YmgB may be a non-specific DNA-binding protein. Using nickel-enrichment DNA microarrays, we showed that YmgB binds, either directly or indirectly, via a probable ligand, genes important for biofilm formation. To advance our understanding of the function of YmgB, we used X-ray crystallography to solve the structure of the protein to 1.8 A resolution. YmgB is a biological dimer that is structurally homologous to the E. coli gene regulatory protein Hha, despite having only 5% sequence identity. This supports our DNA microarray data showing that YmgB is a gene regulatory protein. Therefore, this protein, which clearly has a critical role in acid-resistance in E. coli, has been renamed as AriR for regulator of acid resistance influenced by indole.
Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance.,Lee J, Page R, Garcia-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W J Mol Biol. 2007 Oct 12;373(1):11-26. Epub 2007 Aug 2. PMID:17765265[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lee J, Page R, Garcia-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W. Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. J Mol Biol. 2007 Oct 12;373(1):11-26. Epub 2007 Aug 2. PMID:17765265 doi:10.1016/j.jmb.2007.07.037
- ↑ Lee J, Page R, Garcia-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W. Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. J Mol Biol. 2007 Oct 12;373(1):11-26. Epub 2007 Aug 2. PMID:17765265 doi:10.1016/j.jmb.2007.07.037
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