NTR:nitrite reductase activity

[gocentral]

There are currently 4 terms used for nitrite reductases: GO:0048307 ! ferredoxin-nitrite reductase activity GO:0050421 ! nitrite reductase (NO-forming) activity GO:0042279 ! nitrite reductase (cytochrome, ammonia-forming) activity GO:0008942 ! nitrite reductase (NAD(P)H) activity

However, in direct assays, the acceptor and product may not be obvious, so a grouping term should be used to annotate. For example: in

http://mic.sgmjournals.org/content/154/4/1218.full

the assay is based on a typical assay based on spectrophotometrically following oxidation of reduced methyl viologen coupled to reduction of the substrate (nitrite).

The proposed new term would be placed above the existing terms and under GO:0016661 ! oxidoreductase activity, acting on other nitrogenous compounds as donors

btw, perhaps "other" is not ideal in that term name! Also, there may be other activities where this is an issue.

Reported by: jimhu

Original Ticket: geneontology/ontology-requests/11659

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

[gocentral]

Added term, but struggling with def

Based on the nitrate reductase term =>

Catalysis of the reaction: nitrite + acceptor = ?? + reduced acceptor.

Not sure I can fill something consistent in ??. Do you have any suggestions.

Checking child term defs has left me more confused.

• Nitrite consistently appears on the right hand side of the reaction equation in these defs.
• nitrite reductase [NAD(P)H] activity: Catalysis of the reaction: ammonium hydroxide + 3 NAD(P)+ + H2O = nitrite + 3 NAD(P)H + 3 H+.
• nitrite reductase (cytochrome, ammonia-forming) activity: Catalysis of the reaction: NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+.
• nitrite reductase (NO-forming) activity: Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
• ferredoxin-nitrite reductase activity: Catalysis of the reaction: NH3 + 2 H2O + 6 oxidized ferredoxin = nitrite + 6 reduced ferredoxin + 7 H+.

Shouldn't these be reversed? - or at least have <=> in place of = ? (Guess this is a more general problem of reversible reactions - just, perhaps naively, it seems on to call something a reductase rather than an oxido-reducatse if not specifying direction.

Also - is there an EC mapping? Haven't been able to find one.

Original comment by: dosumis

[gocentral]

• status: open --> closed-fixed

Original comment by: dosumis