PDBsum entry 2oxl

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Gene regulation PDB id
Protein chains
62 a.a. *
BOG ×2
Waters ×31
* Residue conservation analysis
PDB id:
Name: Gene regulation
Title: Structure and function of the e. Coli protein ymgb: a protei for biofilm formation and acid resistance
Structure: Hypothetical protein ymgb. Chain: a, b. Fragment: ymgb c-terminal fragment. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ymgb. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.216     R-free:   0.238
Authors: R.Page,W.Peti,T.K.Woods,J.M.Palermino,O.Doshi
Key ref:
J.Lee et al. (2007). Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance. J Mol Biol, 373, 11-26. PubMed id: 17765265 DOI: 10.1016/j.jmb.2007.07.037
20-Feb-07     Release date:   30-Oct-07    
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Protein chains
Pfam   ArchSchema ?
P75993  (ARIR_ECOLI) -  Probable two-component-system connector protein AriR
88 a.a.
62 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular response to acid   2 terms 


DOI no: 10.1016/j.jmb.2007.07.037 J Mol Biol 373:11-26 (2007)
PubMed id: 17765265  
Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance.
J.Lee, R.Page, R.García-Contreras, J.M.Palermino, X.S.Zhang, O.Doshi, T.K.Wood, W.Peti.
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.
  Selected figure(s)  
Figure 2.
Figure 2. Structure of YmgB. (a) Structure of the YmgB dimer. Chain A, pink, chain B, blue. N and C termini are labeled. (b) Residues (shown as sticks) of the YmgB monomer that form the hydrophobic core, as determined by a loss of solvent-accessible surface area (ASA, GETAREA1.1). Residues in are purple are conserved in the YmgB family of proteins (see Figure 3). (c) Residues (shown as sticks) that are buried upon dimerization and constitute the dimerization interface. 1326 Å^2 of ASA is buried upon dimer formation. (d) Electrostatic surface of the YmgB dimers prepared with MolMol.^72 The YmgB dimer is characterized by an extensive acidic patch (red), which extends around the long axis of the dimer. Small basic patches (blue) punctuate the remainder of the surface. The initial orientation of the dimer surface is shown as a ribbon model on the left.
Figure 5.
Figure 5. DNA-binding assays: YmgB (7 and 9.9 kDa, N-terminal proteolytically cleaved and uncleaved, respectively) bind to (a) crp (candidate identified with nickel-enrichment DNA microarrays); (b) rpsV (identified with both regular DNA microarrays and nickel-enrichment DNA microarrays); (c) lsrF (identified with nickel-enrichment DNA microarrays) and (d) gadA (identified with microarray) promoters. (e) YmgB does not bind to the EBNA DNA. The significant difference in these experiments is the length of the DNA fragments used for the binding studies. The EBNA DNA fragment is much shorter (60 bp) than the 200–300 bp fragments used for the experiments in (a)–(d), indicating that the interaction requires a longer DNA fragment, which is characteristic for geometric DNA recognition. Thus, at least a DNA fragment longer or equal to 60 bp is required for DNA binding. To confirm these results, binding to an unrelated but long DNA fragment was tested. (f) YmgB binds the ycfR promoter, which has not been identified as an interaction candidate. The length (bp) of the used DNA fragment is similar to the DNA fragments used in experiments (a)–(d), and therefore provides evidence that YmgB binds indirectly unspecific DNA fragments either directly or, most likely via a geometric recognition. This method is the same as that used by H-NS (see the text). In all assays: lane 1, labeled DNA of crp, rpsV, lsrF, and gadA etc; lane 2, labeled DNA + YmgB-7 kDa (proteolytically cleaved, see Figure S3 and the text); lane 3, labeled DNA + YmgB-9.9 kDa; arrows (←) highlight YmgB-bound DNA.
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 373, 11-26) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21268264 J.Mukherjee, S.Y.Ow, J.Noirel, and C.A.Biggs (2011).
Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms.
  Proteomics, 11, 339-351.  
19966025 J.Y.Lim, H.J.La, H.Sheng, L.J.Forney, and C.J.Hovde (2010).
Influence of plasmid pO157 on Escherichia coli O157:H7 Sakai biofilm formation.
  Appl Environ Microbiol, 76, 963-966.  
19833773 M.M.Weber, C.L.French, M.B.Barnes, D.A.Siegele, and R.J.McLean (2010).
A previously uncharacterized gene, yjfO (bsmA), influences Escherichia coli biofilm formation and stress response.
  Microbiology, 156, 139-147.  
19172264 C.Attila, A.Ueda, and T.K.Wood (2009).
5-Fluorouracil reduces biofilm formation in Escherichia coli K-12 through global regulator AriR as an antivirulence compound.
  Appl Microbiol Biotechnol, 82, 525-533.  
19168658 J.Lee, T.Maeda, S.H.Hong, and T.K.Wood (2009).
Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones.
  Appl Environ Microbiol, 75, 1703-1716.  
19240136 N.Tschowri, S.Busse, and R.Hengge (2009).
The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli.
  Genes Dev, 23, 522-534.  
19216750 R.A.Notebaart, P.R.Kensche, M.A.Huynen, and B.E.Dutilh (2009).
Asymmetric relationships between proteins shape genome evolution.
  Genome Biol, 10, R19.  
19125816 T.K.Wood (2009).
Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling.
  Environ Microbiol, 11, 1.  
18528414 J.Lee, X.S.Zhang, M.Hegde, W.E.Bentley, A.Jayaraman, and T.K.Wood (2008).
Indole cell signaling occurs primarily at low temperatures in Escherichia coli.
  ISME J, 2, 1007-1023.  
18545668 R.García-Contreras, X.S.Zhang, Y.Kim, and T.K.Wood (2008).
Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes.
  PLoS ONE, 3, e2394.  
18309357 X.S.Zhang, R.García-Contreras, and T.K.Wood (2008).
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA).
  ISME J, 2, 615-631.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.