Dear Gottfried,
I am the lead developer on this standardisation project so I will try to
answer your questions:
1. To standardise the handling of protein modifications, all
modifications are being grouped into categories based on their chemical
structure and context. All modifications within each category are being
handled in the same way, whereas the handling of modifications differs
between modification categories. For example, phosphorylation is handled
as a single chemical unit that includes both modification group and
peptide residue (e.g. SEP). In contrast, all hemes are handled as being
a separate chemical unit that is covalently linked to the peptide
residue (e.g. HEC).
We now have a process in our annotation pipeline to identify protein
modifications and categorise them. When a new modification enters the
archive it will be assessed manually to decide the best way to
consistenly handle it. This means that either way you deposit the new
protein modification, an annotator will review and decide how best to
handle it.
As Paul mentioned, a more detailed description of the project can be
found here:
https://github.com/wwPDB/protein-modification-extension/tree/main
2-3. CAC already exists in the archive and has been observed covalently
linked to Lysine. In this case it was handled as CAC covalently linked
to LYS, so as two separate chemical units. The modification is described
in the PCM category "Covalent chemical modification". If possible I
would try to submit the structure maintaining this format (so splitting
the modified residue into SER + CAC). If this is not possible then this
can be handled by a PDB biocurator during the annotation process.
4-5. I don't know the simplest way to chop a residue into two groups.
However, if you've already deposited a structure where SER + CAC are
described as a single chemical unit then you don't need to separate them
and resubmit the structure. It would be best to message the biocurators
that are working on the structure and ask them to modify the entry.
I hope this helps answer your questions. Let me know if anything remains
unclear.
Kind regards,
Marcus Bage
On 15/10/2024 16:19, Palm, Gottfried wrote:
Dear all,
I have a couple of questions regarding deposition of a structure
with a posttranslational modification.
1. I understand, that PCMs (protein chemical modifications) and PTMs
are now handled in a standard way, but what is the standard way? Is
there a link giving insight into these rules?
2. Specifically, I have a cacodylate (dimethylarsenic acid) modified
serine. A very similar modification, phosphoserine, has its own three
letter code, SEP. The cacodylate modification is handled as serine and
cacodylate (CAC) with a link record (in entry 1LZK). What is the
correct handling?
3. For SER-CAC I could not find an existing link.cif file for
refinement. I rather created a DRG.cif file for the modified serine
and used this for refmac and coot. This works, but how should I
deposit this? The modified residue would clash with the existing
combination of SER / CAC / SER-CAC link.
4. Can I exchange the modified serine by a serine plus cacodylate in
the cif file without going through refmac (I don't have the link.cif
file)? In pdb format I would simply exchange the ATOM lines, but in
cif format?
5. Once I have a cif file with separate SER and CAC residues, I have
to reupload the renamed coordinates again in the deposition process,
thereby loosing all extra information I typed in already. Can I
prevent this loss? (ok, that's a minor problem)
Best rergards
Gottfried
Dr. Gottfried Palm
Universität Greifswald
Inst. für Biochemie (MNF)
Synthetische und Strukturelle Biochemie
Felix-Hausdorff-Straße 4
17489 Greifswald
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--
-------------------------------------------------------------------
Marcus Bage, Ph.D.
Bioinformatician
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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