TolA and TonB

Reference: EMBO J. 21:4207-4218, 2002.
  1. The structure of the C-terminal domain of Pseudomonas aeruginosa TolA is available from the PDB. The PDB code is 1lr0.
  2. Go to the HOMSTRAD top page and type in 1lr0.
  3. Go to the page for the entry hs1lr0a. Examine the structure by clicking the rasmol icon and annotated sequence. See here for key to JOY annotations.
  4. Click the 'pir' link to obtain the sequence.
    >P1;hs1lr0a
    structureX:1lr0:   3 :A: 128 :A:tola protein:Pseudomonas aeruginosa:1.91:18.3
    ALAELLSDTTERQQALADEVGSEVTGSLDDLIVNLVSQQWRRPPSARNGSVEVLIELPDGTITNASVS
    RSSGDKPFDSSAVAAVRNVGRIPEQQLPRATFDSLYRQRRIIFKPEDLSLHHHHH*
    
  5. Exclude the first alpha-helix and the C-terminal his-tag and submit the rest of the sequence to the FUGUE server.

    Paste the following sequence in the input sequence textbox, type in your e-mai address and simply click the 'Search!' button.

    WRRPPSARNGSVEVLIELPDGTITNASVS
    RSSGDKPFDSSAVAAVRNVGRIPEQQLPRATFDSLYRQRRIIFKPEDLSL
    
    You can also check the last option box at the bottom of the page, saying
    Search also against a representative set of PDB chains (slower and experimental - known as FUGUE3 (or FUGUE2.1) in CAFASP3)
  6. You should receive an e-mail message like this.
  7. The results are copied here.

    The 'View Ranking' section lists top hits. The significance of Z-scores is explained at the top of the page:

    Recommended cutoff  : ZSCORE >=    6.0  (CERTAIN   99% confidence)
    Other cutoff        : ZSCORE >=    4.0  (LIKELY    95% confidence)
    Other cutoff        : ZSCORE >=    3.5  (MARGINAL  90% confidence)
    Other cutoff        : ZSCORE >=    2.0  (GUESS     50% confidence)
    Other cutoff        : ZSCORE < 2.0  (UNCERTAIN)  
    
    The 'View Alignments' section provides sequence-structure alignments in various formats.

    Click here for more detailed information on the output page.

  8. Examine the superposition of TolA and domain-swapped TonB structures.

Kenji Mizuguchi
Last modified: Fri Feb 28 11:14:06 GMT 2003