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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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NTR - GPI-modified #4229

Closed deustp01 closed 1 year ago

deustp01 commented 2 years ago

New term requests for GPI-modified carboxyterminal amino acid residues.

[FIGURE] There is currently a term, CHEBI:143797 GPI-anchor amidated amino acid carboxyl end residue(1-), with definition A GPI-anchor amidated amino acid where R1 can be an alkyl or an acyl group, R2 is an acyl group, R3 can be an acyl group or an H, R4-8 can be other sugar groups, phosphoethanolamine or H. The term has seven is_a children, for specific amino acid residues (note: could the definition for 143797 be edited to note that R9 is the side chain of the amino acid carboxyl end residue?): GPI-anchor amidated L-alanine residue(1−) (CHEBI:143785) MOD:00172 GPI-anchor amidated L-asparagine residue(1−) (CHEBI:143786) MOD:00167 GPI-anchor amidated L-aspartate residue(2−) (CHEBI:143787) MOD:00168 GPI-anchor amidated L-cysteine residue(1−) (CHEBI:143798) MOD:00169 GPI-anchor amidated L-serine residue(1−) (CHEBI:143800) MOD:00171 GPI-anchor amidated L-threonine residue(1−) (CHEBI:143801) MOD:00173 GPI-anchor amidated glycine residue(1−) (CHEBI:143799) MOD:00170

[FIGURE] As reviewed by Kinoshita (2020 PMID: 32156170), figure 3, several of the steps of the synthesis of a mature GPI-conjugated protein involve modifications to R3 to remove an acyl group and replace it with a hydrogen atom (step 17), and then the replacement of that hydrogen with a fresh acyl group (step 18). The current terms, allowing either H or acyl at R3, correspond to both the inputs and the outputs of these reactions. To annotate these steps properly Reactome, could we have two children of each of the current eight terms (generic terms and seven amino-acid-specific ones), one with R3 replaced by a hydrogen atom and one in which it is an acyl group?

The attached Word document includes the two figures, showing the structure of CHEBI:143797 and the relevant steps of the GPI pathway described by Kinoshita.

Thanks New term requests for GPI-aminoacid residues.docx

deustp01 commented 1 year ago

We have found a good workaround for our annotation purposes, so these requested terms are not needed at present - closing this ticket. Thanks Peter