2oxl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:26, 30 October 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2oxl.png|left|200px]]
 
-
<!--
+
==Structure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance==
-
The line below this paragraph, containing "STRUCTURE_2oxl", creates the "Structure Box" on the page.
+
<StructureSection load='2oxl' size='340' side='right'caption='[[2oxl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</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>
-
{{STRUCTURE_2oxl| PDB=2oxl | SCENE= }}
+
<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>
 +
== 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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<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/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2oxl ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance===
+
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<ref>PMID:17765265</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_17765265}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2oxl" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 17765265 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17765265}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2OXL is a 2 chains structure of sequences from [http://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].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:17765265</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Doshi, O.]]
+
[[Category: Large Structures]]
-
[[Category: Page, R.]]
+
[[Category: Doshi O]]
-
[[Category: Palermino, J M.]]
+
[[Category: Page R]]
-
[[Category: Peti, W.]]
+
[[Category: Palermino JM]]
-
[[Category: Woods, T K.]]
+
[[Category: Peti W]]
-
[[Category: Acid resistance]]
+
[[Category: Woods TK]]
-
[[Category: Bacterial protein]]
+
-
[[Category: Biofilm]]
+
-
[[Category: Dimer]]
+
-
[[Category: Dna binding protein]]
+
-
[[Category: Gene regulation]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:35:33 2009''
+

Current revision

Structure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance

PDB ID 2oxl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2oxl"
Personal tools