copper-exporting ATPase

[gocentral]

GO:0004008

Current definition:Catalysis of the reaction: ATP + H2O

• Cu2+(in) = ADP + phosphate + Cu2+(out). A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. This bacterial and mammalian enzyme exports copper ions from cells.

This enzyme has also been found in plants. See: PMID: 10319818. Also, from reading the literature, it looks like the copper ions are transported within the cell in yeast and mammalian systems.

Do we need a new term: 'copper-transporting ATPase' or can we modify the string of the existing term to be this and modify the definition to remove the last sentence?

There are six annotations to this term.

1 FlyBase 2 SPTr 1 SGD 2 TIGR_Ath

Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/629":https://sourceforge.net/p/geneontology/ontology-requests/629

[gocentral]

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Hi Tanya, I wouldn't say the definition of GO:0004008 states explicitly where the transport occurs. The second part of the definition (starting "A P- type ATPase...") does, but I would class this as extra information about specific gene products. It doesn't add anything to the definition of the function itself (ie. Cu export and ATP -> ADP) and could be deleted. As long as your ATPase is moving copper out of some part of the cell, I think it's OK to annotate to GO:0004008.

This bring up the question of whether GO:0004008 and similar terms are actually two functions: copper export and ATPase activity...

Original comment by: girlwithglasses

[gocentral]

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Hi Amelia,

OK. If we can amend the last sentence to read: "In bacterial and mammalian cells, this enzyme exports copper ions from the cell." , I can use this term to annotate plant genes. The word 'this' implies, at least to me, that the enzyme doesn't exist in plants.

Cheers,

Tanya

As for splitting the function, I do see your point. We could see what the group in general thinks. The thing is that the copper export and ATPase activity are linked, there is no export without ATP hydrolysis.

Original comment by: tberardini

[gocentral]

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Hi Tanya and Amelia,

I suggest replacing the last sentence

"This bacterial and mammalian enzyme exports copper ions from cells"

from the existing definition to

"The activity is associated with transport of copper from the cytosol into the lumen of the secretory pathway" Ref: PMID: 9325307 Ref: http://www.jbc.org/cgi/content/full/272/41/25787/F6

should work.

-Pankaj

Original comment by: jaiswalp

[gocentral]

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Hi Pankaj/Amelia,

I like your sentence. Your reference pertains to yeast. For a plant perspective. see also PMID: 10319818 (Fig.8).

What do you think, Amelia? Can we clarify the definition by doing this?

Tanya

Original comment by: tberardini

[gocentral]

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Yep. I used the PMID: 10319818 (Fig.8) to get to my ref. The Arabidopsis study involved complementation assay in Yeast and came up with the same conclusion as suggested by Yeast.

You may also like to have a look at the review article at http://www.sciencedirect.com/science?\_ob=MImg&\_imagekey=B6TCV-3W25902-1H-1&\_cdi=5180&\_orig=brow se&_coverDate=07%2F31%2F1996&_sk=999789992&wchp=dGLbVlz-lSzBV&_acct=C000022719&_version=1 &_userid=492137&md5=d5122032673e2c18ef5527b7e91fb1d6&ie=f.pdf

which proposed for a bifurcation for P-type ATPase activity (GO:0015662),

there are two types of them 1- heavy metal transporting P-type ATPase activity; synonym: CPx-type ATPase 2- non-heavy metal transporting P-type ATPase activity

This might promt for restructuring of existiing GO structre for P-type ATPase activity (GO:0015662).

-Pankaj

Original comment by: jaiswalp

[gocentral]

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Great review article! I agree, let's add two direct children for P-type ATPase activity that can be used to group the existing children.

Tanya

Original comment by: tberardini

[gocentral]

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Great ! This will help. Please go ahead.

-Pankaj

Original comment by: jaiswalp

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Hi guys,

To go back in your discussion a bit, I think it may be better to clip out extra information relating to where the enzyme occurs and just leave it as "Catalysis of the reaction: ATP + H2O + Cu2+(in) = ADP + phosphate + Cu2+(out).". This will prevent any future problems if gene products with this function are found in other species. I would also prefer to remove references to where in the cell gene products with this activity are found (eg. "It exports copper ions from the cell") because it may differ between species / etc.

If you're looking at P-type ATPases, you could add a definition for GO:0015662 (P-type ATPase) at the same time... :-)

Original comment by: girlwithglasses

[gocentral]

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I agree with Amelia's solution - just totally get rid of the last bit of the def - the first bit's the true function anyway. Just so you know Pankaj, I've started working on the ATPase section already so I may be asking you for your input - I think its going to be a fairly long job.

Original comment by: jl242

[gocentral]

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I agree with keeping just the first part of the definition. Thanks!

Original comment by: tberardini

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I have removed all the gene product-specific information to leave the definition as "Catalysis of the reaction: ATP + H2O + Cu2+(in) = ADP

• phosphate + Cu2+(out).".

Original comment by: girlwithglasses

[gocentral]

• labels: --> Other term-related request
• assigned_to: nobody --> girlwithglasses
• status: open --> closed-fixed

Original comment by: girlwithglasses