#9993 cyclin-dependent protein tyrosine kinase activity

None
closed-accepted
5
2014-11-24
2013-02-14
No

Hi, I would like to request the term
cyclin-dependent protein tyrosine kinase activity
suggested def: Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the binding of a regulatory cyclin subunit

there is a term for cyclin-dependent protein kinase activity but this has the parent ser/thr kinase activity.

Discussion

  • Paola Roncaglia

    Paola Roncaglia - 2013-02-15
    • assigned_to: nobody --> paolaroncaglia
     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-16

    Hi Antonia,

    Could you please provide a reference for your new term. Then I'll add it as is_a protein tyrosine kinase activity.

    GO:0004693 cyclin-dependent protein kinase activity is placed as is_a ser/thr kinase activity according to its corresponding Enzyme Commission number (EC 2.7.11.22 is_a EC 2.7.11.- which is 'Protein-serine/threonine kinases'). See this old SF for reference: https://sourceforge.net/tracker/index.php?func=detail&aid=1743484&group_id=36855&atid=440764
    To be honest, nothing in the definition of EC 2.7.11.22 specifies what amino acid is phosphorylated. There are no other cyclin-dependent kinases in EC. So I wonder if this should rather be the generic parent term for your new term. Otherwise, I'd be tempted to rename GO:0004693 as 'cyclin-dependent protein serine/threonine kinase activity', but I'd need to look at annotations... maybe you could ask Val and Midori (who created the term) if they have a quick opinion please?

    I'll add your term when I have a reference, we may deal with GO:0004693 separately if needed.

    Thanks,
    Paola

     
  • Antonia Lock

    Antonia Lock - 2013-02-17

    Thanks, the PMID is 1372994, I'll fwd to Val and Midori

     
  • Valerie Wood

    Valerie Wood - 2013-02-17

    I agree the parentage for the existing term is wrong, it should be general, to match the def.
    It has probably only been used by us for ser/threonine but we can't guarantee for other dbs usage.
    So probably we should also have a serine/threonine child and move existing annotations to the new children as appropriate, if known.

    Alternatively we could have only a general term
    cyclin-dependent protein kinase activity
    and capture all of the residue specificity with our extension an residue annotations.
    (actually this is probably preferable?)

     
  • Antonia Lock

    Antonia Lock - 2013-02-17

    we can't capture specific residues using extensions

     
  • Midori Harris

    Midori Harris - 2013-02-18

    I did not create GO:0004693, and I don't have any specialist knowledge on protein kinases.

    I suspect that the last time anyone worked on GO:0004693 -- which may have been when I updated protein kinase EC dbxrefs in 2007 -- GO curators simply didn't know of any cyclin-dependent protein tyrosine kinases.

    So I think this can be handled according to standard GO practice. Because GO:0004693 has the Ser/Thr-specific meaning implied by its parent, I'd be inclined to rename it ('cyclin-dependent protein serine/threonine kinase activity') and edit its text definition, and create a new term with the non-amino-acid-specific name, definition and parent. I'd also move the EC:2.7.11.22 xref to the new term.

    m

     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-18

    Hi Midori, thanks for your feedback. Antonia, I'll work on this tomorrow. Cheers,
    Paola

     
  • Midori Harris

    Midori Harris - 2013-02-18

    One more thing - I just did a little poking around PubMed and Google a bit, and I'm getting the impression that people tend to refer to cyclin-dependent kinases as Ser/Thr, even in recent pubs (e.g. abstract of PMID: 19145493; I haven't looked at the full text). Might be worth checking with someone who knows this stuff better that me ...

     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-19
    • status: open --> open-accepted
     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-19

    Hello,

    I've added the new term for Antonia, so she may use it to annotate:
    GO:0097469 cyclin-dependent protein tyrosine kinase activity
    is_a GO:0004713 protein tyrosine kinase activity
    (will add generic cyclin-dependent parent as soon as we figure out what that should be -
    leaving this ticket open until then.)

    I'll email Harold and Peter to ask about GO:0004693 cyclin-dependent protein kinase activity.
    Thanks,

    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-27
    • labels: 390929 --> cell cycle
     
  • Paola Roncaglia

    Paola Roncaglia - 2013-02-27

    Update: Harold and Peter don't see any problem with (Midori's) suggested plan of action.
    However we plan to discuss cell-cycle related SF items at the cell cycle meeting this week, so I'll hold on to this for a little more, just to make sure
    (GO:0004693 cyclin-dependent protein kinase activity has quite a few children).

     
  • Paola Roncaglia

    Paola Roncaglia - 2013-03-06

    In the end, we didn't get a chance to discuss this at the cell cycle meeting last week.
    However, I've implemented Midori's suggestion:

    "...So I think this can be handled according to standard GO practice. Because GO:0004693 has the Ser/Thr-specific meaning implied by its parent, I'd be inclined to rename it ('cyclin-dependent protein serine/threonine kinase
    activity') and edit its text definition, and create a new term with the non-amino-acid-specific name, definition and parent. I'd also move the EC:2.7.11.22 xref to the new term."

    My preference for this option is based
    - on the serine/threonine parent;
    - on this reference from 2009 (also from Midori): PMID:19145493 ("Cyclin-dependent kinases (CDKs) are serine/threonine protein kinases..." (http://www.ncbi.nlm.nih.gov/pubmed/?term=19145493);
    - on the wikipedia entry: "...CDKs phosphorylate their substrates on serines and threonines, so they are serine-threonine kinases. ..." (http://en.wikipedia.org/wiki/Cyclin-dependent_kinase) The reference provided for this assertion is David Morgan's cell cycle textbook.

    So, summing up:

    Edited GO:0004693 cyclin-dependent protein kinase activity so it refers to serine/threonine specificity;

    (To be on the safe side, I've left the EC xref attached to GO:0004693)

    Edited children of GO:0004693 cyclin-dependent protein serine/threonine kinase activity
    so their new names, defs and parentage reflect the serine/threonine specificity;

    Added new term:
    GO:0097472 cyclin-dependent protein kinase activity

    Added links:
    GO:0097469 cyclin-dependent protein tyrosine kinase activity
    and
    GO:0004693 cyclin-dependent protein serine/threonine kinase activity
    both are is_a
    GO:0097472 cyclin-dependent protein kinase activity

     
  • Paola Roncaglia

    Paola Roncaglia - 2013-03-06

    (continues from my last comment below)
    However, some terms still remain that contain the string 'cyclin-dependent protein kinase' in their names. These likely need editing too, so I'm leaving this item open until I can check/fix them.

     
  • Paola Roncaglia

    Paola Roncaglia - 2014-06-18

    All done now, closing, thanks.

     
  • Paola Roncaglia

    Paola Roncaglia - 2014-06-18
    • labels: cell cycle --> cell cycle, Other term-related request
    • status: open-accepted --> closed-accepted
    • Group: --> None
     
  • Valerie Wood

    Valerie Wood - 2014-11-24

    Not sure, this hasn't been used in annotation, will check and get back to you. If it isn't used I think we need to go back. It was probably a misunderstanding. Wee1 is a cyclin-dependent kinase kinase, not a cyclin-dependent kinase ;)

    Val

     

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