Retrieving oxyanion hole residues positions from UniProt or PDB databases

Question

[Mariana]

Hello!

I was wondering how can i retrieve oxyanion hole residues positions from UniProt or PDB databases. I have a protein database curated by a past member of my lab that comprises information on plastic degrading hydrolases. One of the main characteristics of these enzymes is the presence of oxyanion hole residues.

In that database, there are 2 columns "OxyanionHole Uniprot" and "OxyanionHole PDB" witth the respective positions retrieve from both databases.

I have been searching in UniProt and PDB entries and can't find this informarion.

An exaple of an accession id that I have information on in my database:

UniProt: A0A0K8P6T7
PDB: 5XFZ
Oxyanionhole(PDB): Y59;M133 
Oxyanionhole(UniProt): Y87;M161 

Thank you in advance!

[GenoMax]

Per ChatGPT:

The annotation of the oxyanion hole in protein databases such as the Protein Data Bank (PDB) and UniProt is typically done through a combination of structural and functional descriptions, though it is not always explicitly labeled as "oxyanion hole" in these databases.

Ask GPT "how is oxyanion hole annotated in PDB or UniProt" to see full details, while we wait on someone with direct knowledge to respond.

Your colleague may have manually annotated the data.

[me]

Following up on GenoMax I think this is custom annotations. Your example does not seem to exist. Nor did it in any of the historical versions of that entry I selected.

Answer 1

[me]

You can find these kinds of sites in UniProt annotation using a SPARQL query like

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT
?protein ?comment ?rhea
WHERE {
  ?protein up:annotation ?siteAnnotation   , ?catalyticActivityAnnotation .
  ?catalyticActivityAnnotation a up:Catalytic_Activity_Annotation ; up:catalyticActivity ?catalyticActivity .
  ?catalyticActivity up:catalyzedReaction ?rhea .
  ?siteAnnotation a up:Site_Annotation ;
                  rdfs:comment ?comment .
  FILTER(REGEX(?comment, "oxyanion", "i") && REGEX(?comment, "hole", "i")
}

This unfortunately is very slow on the official UniProt SPARQL endpoint. But on a server hosted by the Qlever team, this is fast although on slightly out of date data.

For PDB you should be able to get the same kind out of data using the PDBj SPARQL endpoint.

Answer 2

[Elisabeth Gasteiger]

I'm not sure I understand the question, but indeed the UniProtKB entry A0A0K8P6T7 has binding sites annotated in the 2 mentioned positions, Y-87 and M-161, as well as for W-185:

Binding: poly(ethylene terephthalate) CHEBI:13170

Here is how binding sites are annotated , and how you can search UniProtKB for chemical or reaction data

Don't hesitate to contact the UniProt helpdesk if you have more specific questions.