carB

UniProt ID: Q88DU6
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
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Gene Description

carB encodes the ATP-dependent large chain of carbamoyl-phosphate synthase. Together with the glutaminase chain CarA it produces carbamoyl phosphate for de novo UMP and L-arginine biosynthesis; the large chain can also use free ammonia in the component reaction.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
IEA
GO_REF:0000120 		ACCEPT
Summary: CarB catalyzes ATP-dependent carbamoyl-phosphate formation using free ammonium in the isolated large-chain reaction.
Reason: Rhea 18029 is explicitly assigned in the reviewed record.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
large (or ammonia) chain to synthesize carbamoyl phosphate.
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
IEA
GO_REF:0000120 		REMOVE
Summary: CarB is the ATP-dependent catalytic chain of the CarAB glutamine-dependent synthase.
Reason: The enables relation is incorrect because CarB performs the ATP-dependent synthetic component and does not catalyze glutamine hydrolysis by itself. A separate contributes_to row captures its role in the complete CarAB reaction.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
Large subunit of the glutamine-dependent carbamoyl phosphate
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
ISS
file:PSEPK/carB/carB-uniprot.txt 		NEW
Summary: CarB contributes the ATP-dependent synthetic component of the two-chain CarAB activity.
Reason: CarB uses the ammonia supplied by CarA, so its relationship to the complete glutamine-dependent synthase activity is contributes_to.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
Large subunit of the glutamine-dependent carbamoyl phosphate
GO:0005524 ATP binding
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: CarB consumes two ATP molecules during carbamoyl-phosphate formation.
Reason: ATP interaction is required for catalysis but is less informative than the synthase activities.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
involved in binding the 2 ATP molecules needed for carbamoyl phosphate
GO:0005737 cytoplasm
IEA
GO_REF:0000118 		KEEP AS NON CORE
Summary: CarB is a soluble biosynthetic enzyme expected in the bacterial cytoplasm.
Reason: Plausible and useful localization, but secondary to the catalytic and pathway annotations.
GO:0006520 amino acid metabolic process
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: CarB supplies carbamoyl phosphate to arginine biosynthesis, but this parent process is overly broad.
Reason: Retain the specific L-arginine biosynthetic process.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
PATHWAY: Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl
file:PSEPK/carB/carB-deep-research-openscientist.md
Carbamoyl phosphate is the single shared precursor that feeds **both the arginine biosynthetic pathway and the pyrimidine nucleotide biosynthetic pathway**.
GO:0006526 L-arginine biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: CarAB supplies carbamoyl phosphate to L-arginine biosynthesis.
Reason: This pathway branch is explicitly assigned in the reviewed record.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
PATHWAY: Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl
GO:0006541 L-glutamine metabolic process
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: The CarAB holoenzyme consumes glutamine, but this broad process does not describe CarB's direct chemistry.
Reason: Retain the UMP and arginine biosynthetic processes as the informative pathway assignments.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
the small (or glutamine) chain
GO:0044205 'de novo' UMP biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: CarB contributes the first reaction of de novo UMP biosynthesis.
Reason: This pathway branch is explicitly assigned in the reviewed record.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
file:PSEPK/carB/carB-deep-research-openscientist.md
Carbamoyl phosphate is the single shared precursor that feeds **both the arginine biosynthetic pathway and the pyrimidine nucleotide biosynthetic pathway**.
GO:0046872 metal ion binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: CarB requires magnesium for the ATP-dependent reaction.
Reason: Metal binding is a catalytic requirement but not the primary molecular function.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
Note=Binds 4 Mg(2+) or Mn(2+) ions per subunit.
GO:0005951 carbamoyl-phosphate synthase complex
ISS
file:PSEPK/carB/carB-uniprot.txt 		NEW
Summary: CarB is the ATP-dependent chain of the two-chain carbamoyl-phosphate synthase complex.
Reason: The reviewed record explicitly describes the enzyme as a two-chain complex.
Supporting Evidence:
file:PSEPK/carB/carB-uniprot.txt
Composed of two chains; the small (or glutamine) chain

Core Functions

CarB uses ATP, hydrogencarbonate, and ammonia supplied by CarA to form carbamoyl phosphate for UMP and arginine biosynthesis.

Molecular Function:
carbamoyl-phosphate synthase (ammonia) activity
Directly Involved In:
'de novo' UMP biosynthetic process L-arginine biosynthetic process
In Complex:
carbamoyl-phosphate synthase complex
Supporting Evidence:
  • file:PSEPK/carB/carB-uniprot.txt
    Large subunit of the glutamine-dependent carbamoyl phosphate
  • file:PSEPK/carB/carB-uniprot.txt
    Composed of two chains; the small (or glutamine) chain

References

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Deep Research

OpenScientist

(carB-deep-research-openscientist.md)

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