I'm studying brain tumors, and one of the most important mutations in this subset of tumor is a mutation in codon 27 of H3F3A gene, supposedly a change from lysine to methionine on codon 27. Surprisingly, it seems that lysine is actually in codon 28 of H3F3A, not in 27. Does anyone may have an idea on how that mutation can happen, or if something makes lysine be counted as codon 27?
I'm guessing the first amino acid (methionine) is excluded, since that first residue is usually removed in mature proteins.
Dear Dr Paulo Oliveira-Costa
I agree with Dr Hepler.
I cannot see any other way a second codon position A->T can be so numbered.
Is this some convention with this particular protein? While the first Met may be removed in mature proteins IMHO it is unwise to assume that this is the case for all proteins and that the initial Met is included in the counting. As far as I can tell other workers seem to agree with me on this point.
There is another possibility. Strings may be numbered either with a zero base or a one base. Consider the string MAGR
If we use a zero base then G is at position 2. If we use a one base then G is at position 3.
This always causes problems when programming. Visual Basic offers a choice between base one and base zero. Most languages follow the C convention of numbering strings with base zero.
It is possible that the authors who used this numbering were following the base zero convention rather than the base one.
Also, sometimes the amino acids in a protein are numbered so that they match the numbering in the ortholog in another species. For example, if the mouse version of a protein has one more amino acid at the N-terminus than the human version of a protein, then the first amino acid in the human protein might be called amino acid 2.
David does bring up a good point. Whoever first described this mutation used a specific notation, which has remained prevalent in the community. I don't think its very common to indicate the first residue, as a 0 as that's a little misleading, but it would certainly explain the phenomenon.
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