Activity Prediction Database for

Mutants of Bacteriophage T4 Lysozyme

The wild-type (wt) amino acid sequence of T4 lysozyme is based on that of the Protein Data Bank (PDB)1 entry 3lzm. The primary sequence of 3lzm is given below.
T4 lysozyme sequence

 wt amino acid
 position number
 substitution
 number of  classes (2 or 4)
mutant #1
mutant #2
mutant #3
mutant #4
mutant #5

First choose the wt amino acid residue (1 letter code), the corresponding residue number (1-164), and any one of the 19 possible residue substitutions of the wt residue (1 letter code). Next, choose the number of activity classes (2 or 4). For the two-class case, the activity of a mutant is considered to be either "active" or "inactive". Using four classes, the mutant activity labels are "high", "medium", "low", or "negative". Repeat for up to five single-point mutants of T4 lysozyme. Finally, click on the "Check Activity Levels" button to obtain the predicted activity levels of the requested T4 lysozyme mutants. All predictions are based on decision tree models generated by using residual profile2 vectors for a training set of 2015 T4 lysozyme mutants with experimentally measured activity levels. Decision tree models based on the 1-against-all method are used for making the four-class predictions. The activity levels for the training set data (those with "known" activity when queried above) can be located in Rennell et al.3

References

  1. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
  2. Masso M. & Vaisman I. (2007). Accurate prediction of enzyme mutant activity based on a multibody statistical potential. Bioinformatics, 23, 3155-3161.
  3. Rennell, D., Bouvier, S. E., Hardy, L. W. & Poteete, A. R. (1991). Systematic mutation of bacteriophage T4 lysozyme. J. Mol. Biol. 222, 67-88.