A TATA-box binding protein

1. PatchFinder requires the PDB ID (or a supplemented PDB file) as input. In the example below we used chain A at PDB ID 1qn7¹ which is the structure of a TATA-box binding protein. A Multiple Sequence Alignment (MSA) with the sequence of the query protein was created using BLAST². The name of the query sequence in the CLUSTAL W formatted MSA is '1qn7_A'.

The input form should be filled as follows:

Figure 1:

The input alignment is available over here.

2. After a few minutes (usually up to an hour) an E-mail notification with a link to the result page is sent.

An example of a result page can be seen here.

Figure 2:

The visualization of the results uses FirstGlance in Jmol.

3. The TATA-box binding protein on Figure 3a is colored according to the conservation as computed by ConSurf³ the DNA is colored orange. Figure 3b shows the patches found by PatchFinder. The best patch is colored red and the second best patch is colored blue while the rest of the molecule is grey. Even though the DNA-binding site is apparently symmetric, the ML-patch does not cover the whole binding site. Examining this asymmetry, it turns out that the transcription initiation efficiency is much more dependent on the identity of the nucleotides which bind the ML-patch, than the nucleotides which bind the second best patch.

Figure 3:

References:

1. Patikoglou, G. A., Kim, J. L., Sun, L., Yang, S. H., Kodadek, T. & Burley, S. K. (1999). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 13, 3217-30.

2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389-402.

3. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. & Ben-Tal, N. (2005). ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33, W299-302.