pyrC

UniProt ID: Q88NW7
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
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Gene Description

pyrC encodes a zinc-dependent dihydroorotase that reversibly cyclizes N-carbamoyl-L-aspartate to (S)-dihydroorotate, completing pyrimidine ring closure in de novo UMP biosynthesis.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004151 dihydroorotase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: PyrC catalyzes reversible ring closure between carbamoyl aspartate and dihydroorotate.
Reason: The reviewed UniProt entry assigns EC 3.5.2.3 and Rhea 24296.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
Catalyzes the reversible cyclization of carbamoyl aspartate
PMID:8572888
hydrolyzed dihydro-L-orotate and its methyl ester, and the reactions were
file:PSEPK/pyrC/pyrC-deep-research-openscientist.md
The gene **pyrC** (ordered locus **PP_1086**; UniProt **Q88NW7**; *PYRC_PSEPK*) of *Pseudomonas putida* KT2440 encodes **dihydroorotase (DHOase; EC 3.5.2.3)**
GO:0005737 cytoplasm
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: Cytoplasm is a broad parent of the more informative cytosol annotation.
Reason: Retain cytosol as the narrower soluble-enzyme location.
GO:0005829 cytosol
IEA
GO_REF:0000118 		KEEP AS NON CORE
Summary: PyrC is a soluble biosynthetic enzyme expected in the bacterial cytosol.
Reason: Plausible and more specific than cytoplasm, but secondary to the catalytic and pathway annotations.
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: PyrC acts in de novo pyrimidine synthesis.
Reason: Retain the more specific de novo UMP process.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
GO:0006221 pyrimidine nucleotide biosynthetic process
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: This process parent is correct but broad.
Reason: Retain de novo UMP biosynthesis.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
GO:0008270 zinc ion binding
IEA
GO_REF:0000104 		KEEP AS NON CORE
Summary: PyrC binds two zinc ions per subunit.
Reason: Zinc binding supports catalysis but is not the primary molecular function.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
Binds 2 Zn(2+) ions per subunit.
PMID:8572888
The enzyme was inhibited by metal ion chelators and activated by
GO:0016787 hydrolase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Generic hydrolase activity is less informative than dihydroorotase activity.
Reason: Retain GO:0004151.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
EC=3.5.2.3
GO:0016812 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: This hydrolase parent is correct but less specific than dihydroorotase activity.
Reason: Retain GO:0004151.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
EC=3.5.2.3
GO:0019856 pyrimidine nucleobase biosynthetic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: This process parent is broad relative to de novo UMP synthesis.
Reason: Retain GO:0044205.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
GO:0044205 'de novo' UMP biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: PyrC performs pyrimidine ring closure in de novo UMP synthesis.
Reason: The reviewed record assigns step 3 of 3 from bicarbonate to dihydroorotate.
Supporting Evidence:
file:PSEPK/pyrC/pyrC-uniprot.txt
(S)-dihydroorotate from bicarbonate: step 3/3.

Core Functions

PyrC cyclizes N-carbamoyl-L-aspartate to (S)-dihydroorotate in de novo UMP biosynthesis.

Molecular Function:
dihydroorotase activity
Directly Involved In:
'de novo' UMP biosynthetic process
Supporting Evidence:
  • file:PSEPK/pyrC/pyrC-uniprot.txt
    Catalyzes the reversible cyclization of carbamoyl aspartate
  • PMID:8572888
    hydrolyzed dihydro-L-orotate and its methyl ester, and the reactions were
  • file:PSEPK/pyrC/pyrC-deep-research-openscientist.md
    The gene **pyrC** (ordered locus **PP_1086**; UniProt **Q88NW7**; *PYRC_PSEPK*) of *Pseudomonas putida* KT2440 encodes **dihydroorotase (DHOase; EC 3.5.2.3)**

References

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Suggested Questions for Experts

Q: Does PP_1086 encode the same dihydroorotase purified in the classic species-level P. putida study, and is it the sole source of this activity in KT2440?

Suggested Experiments

Experiment: Delete PP_1086 and test pyrimidine auxotrophy, uracil rescue, and loss of dihydroorotase activity; complement with Q88NW7 to connect the classic P. putida enzymology directly to the KT2440 locus.

Type: genetics and biochemical complementation

Deep Research

OpenScientist

(pyrC-deep-research-openscientist.md)

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