peroxidase activity (rev. req)

[gocentral]

Hi,

It appears that GO:0016684 (oxidoreductase activity, acting on peroxide as acceptor) tree needs reorganization by having three top level terms..

for Class-I/II/III types

More on this specially in plants. Ref: European Journal of Biochemistry Volume 269 Issue 24 Page 6063 - December 2002 doi:10.1046/j.1432-1033.2002.03311.x

and Welinder, K.G. (1992) Superfamily of plant, fungal and bacterial peroxidases. Curr. Opin. Struc. Biol. 2, 388-393.

The bacterium Escherichia coli expresses a single intracellular heme peroxidase with dual catalase-peroxidase activities, a finding confirmed by its genome sequence. Mitochondrial yeast cytochrome c peroxidase, chloroplast and cytosol plant ascorbate peroxidases are rather similar in amino acid sequence to the bacterial enzymes, and they are collectively referred to as class I peroxidases. These intracellular peroxidases appear to function as protective peroxide scavengers and they constitute in plants a small family of 7-10 genes, encoding both soluble and membrane bound enzymes. White-rot fungi like Phanerochaete chrysosporium and Trametes versicolor contain a small gene family encoding approximately 10 different lignin-degrading or Mn-dependent heme peroxidases. In contrast, the ink cap fungus Coprinus cinereus contains only a single peroxidase gene. The extracellular fungal peroxidases (class II) can participate in secondary metabolism under conditions of limited nutritional supply. The classical plant peroxidases (class III) are targeted via the endoplasmic reticulum (ER) to the outside of the plant cell or to the vacuole. They are ascribed a variety of functional roles in plant biology, which include lignification, suberization, auxin catabolism, defense, stress and developmentally related processes .

Or may be we do something only for plants..

Also it seems that GO:0016684 (oxidoreductase activity, acting on peroxide as acceptor) is the same as GO:0004601 (peroxidase activity). If so then one of this term becomes obsolete.

Pankaj

Reported by: jaiswalp

Original Ticket: "geneontology/ontology-requests/1327":https://sourceforge.net/p/geneontology/ontology-requests/1327

[gocentral]

Logged In: YES user_id=473796

Pankaj,

Val brought your last point up before - see SF:791851. Your other point refers to particular classes of gene products, not molecular functions. You need to use concurrent annotation to capture the information about the different classes of peroxidase, not new function terms.

Original comment by: girlwithglasses

[gocentral]

• assigned_to: nobody --> girlwithglasses
• status: open --> closed-rejected

Original comment by: girlwithglasses