Robbie Joosten wrote:
Hi Ed,
> Personally I don't care one way or the other, but it may be pointed out
> that if D25 is actually number 37 in a homologous protein, it should be
> D37. Just as acknowledgement of the (somewhat purist) point of view
> that the residue number should denote its linear distance from the
> N-terminus.
>
But which N-terminus should we use? The N-terminus of the protein, the
one of the construct, or the N-terminus of what is ordered in the PDB
file? And what about deletions, isn't it useful to have gaps in the
residue numbering indicating a deletion?
The N-terminus of the nascent polypeptide, or after cleavage of the leader
sequence?
I think having the numbering of key residues be the same across
different species and across different constructs of the same
protein would be much more useful than having the residue number
tell how far you are from the N-terminus. But it takes some
organization between different groups working on the same protein
family, which may be hard to arrange.I remember at an early meeting
of scientists working on cytochrome bc1 it was decided to use the
yeast sequence as standard, but unfortunately this was not followed
by the crystallographers, including myself, so now we have to specify
whether the numbering is that of yeast, beef, chicken, or Rhodobacter.
Getting proper residue numbering is difficult and there will always be
exceptions. Dealing with all the different possible schemes is a
nightmare. That is why residue numbering is always one of the first
topics in structural bioinformatics. The PDB now seems to follow the
numbering from UniProt which makes things a lot clearer, but fusion
proteins now lead to crazy jumps in the residue numbering resulting in
chains with numbers going from 100, to 1200 and back to 300.
For many well studied groups of proteins insertion codes help the
biological interpretation of the structures. Unfortunately, insertion
codes are surprisingly poorly supported by software that uses PDB files
especially outside crystallography (but even CCP4 software has some
remaining problems). I hope this thread will at least increase awareness
of the existence of insertion codes. It is very much needed...
Cheers,
Robbie
>
> Cheers,
>
> Ed.
>
> --
> "Hurry up before we all come back to our senses!"
> Julian, King of Lemurs
