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closeThe protein described isn't YopM
Posted by JMcPhee on 05 May 2010 at 17:17 GMT
The YopM protein does not contain an E3 ubiquitin ligase domain. It consists exclusively of leucine-rich repeats (LRR). There are 5-6 YopM homologs (depends on the strain examined) that have an N-terminal LRR domain and a C-terminal E3 ligase domain. It is important to state the accession number or the commonly used protein IDs when referring to proteins, otherwise it is impossible to know which protein this work is referring to. The one thing that is clear, is that it is NOT YopM, as named throughout the paper.
Also, while it is true that YopM interacts with RSK1 and PKN2 (as described in Fig 6D) it is not known whether the other YopM homologs do... thus it is difficult to know how much weight to put on the interpretations of RSK1 interactions with the protein described, since the protein the authors are describing is not YopM.
The actual meat of the paper (i.e. - defining protein folds) seems like a useful algorithm, but I think that in trying to stretch the work to a specific example, the authors may have gone a little bit off-course.