RefGenome Electronic Jamboree 2009-02 CAD

From GONUTS

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Orthoset

EcoliWiki has included the carA gene product annotations. The CarA gene product is a subunit of the E. coli carbamoyl phosphate synthetase, but was not included in the ortholog set.

Participants

Name	Group	Organism(s)/Genome(s)	Notes
Ruth Lovering	BHF-UCL	Human	very few papers describe human protein, have annotated hamster protein and used this for ISS
Susan Tweedie	flyBase	D. melanogaster
Varsha Khodiyar	BHF-UCL	Human
Harold Drabkin	MGI	Mouse	Doing ISO to golden hamster protein.
Brenley McIntosh	ecoliwiki	E. coli	P00968 (carB) Carbamoyl-phosphate synthase large chain
Stan Laulederkind	RGD	Rat
Debby Siegele	ecoliwiki	E. coli	P00968 (carB) Carbamoyl-phosphate synthase large chain
Rachael Huntley	GOA	Human	CAD (P27708)
Lakshmi Pillai	AgBase	G. gallus	No ortholog
Kimberly Van Auken	WormBase	C. elegans	pyr-1 (WBGene00004259)
Seval Ozkan	AgBase	other
Petra Fey	dictyBase	D. discoideum	Noticed now that dicty enzyme is rather CAD than CPS
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CAD

Category	ID	Term	Human	Mouse	Rat	Chicken	Zfish	Fly	Worm	Dicty	Dicot	Yeast	Pombe	Ecoli
Molecular Function	GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	ISS	ISS	IDA	X	X	IMP IDA	X	IDA	X	X	X	IGI IMP
Molecular Function	GO:0004070	aspartate carbamoyltransferase activity	ISS	ISS	IDA	X	X	IMP IDA	X	IDA	X	X	X	X
Molecular Function	GO:0019899	enzyme binding	IPI	X	X	X	X	X	X	X	X	X	X	X
Molecular Function	GO:0005524	ATP binding	ISS	ISS	X	X	X	IC	X	X	X	X	X	IMP
Molecular Function	GO:0016597	amino acid binding	ISS	X	X	X	X	IC	X	X	X	X	X	X
Molecular Function	GO:0004151	dihydroorotase activity	ISS	ISS	IDA	X	X	IMP IDA	X	IDA	X	X	X	X
Molecular Function	GO:0004086	carbamoyl-phosphate synthase activity	X	X	X	X	X	X	X	X	X	X	X	IDA
Molecular Function	GO:0005515	protein binding	X	X	X	X	X	X	X	X	X	X	X	IDA IMP
Molecular Function	GO:0046872	metal ion binding	X	X	X	X	X	X	X	X	X	X	X	IDA
Molecular Function	GO:0000166	nucleotide binding	X	X	X	X	X	X	X	X	X	X	X	IMP
Molecular Function	GO:0004672	protein kinase activity	X	ISS	X	X	X	X	X	X	X	X	X	X
Molecular Function	GO:0042802	identical protein binding	X	X	IDA	X	X	X	X	X	X	X	X	X
Molecular Function	GO:0002134	UTP binding	X	ISS	X	X	X	X	X	X	X	X	X	X
Biological Process	GO:0006207	'de novo' pyrimidine base biosynthetic process	ISS	ISS	X	X	X	IMP	X	X	X	X	X	IMP
Biological Process	GO:0018107	peptidyl-threonine phosphorylation	ISS	ISS	X	X	X	X	X	X	X	X	X	X
Biological Process	GO:0046777	protein amino acid autophosphorylation	ISS	ISS	X	X	X	X	X	X	X	X	X	X
Biological Process	GO:0006541	glutamine metabolic process	X	X	X	X	X	IC	X	IDA	X	X	X	IMP
Biological Process	GO:0019856	pyrimidine base biosynthetic process	X	X	X	X	X	X	IMP	X	X	X	X	IMP
Biological Process	GO:0008652	amino acid biosynthetic process	X	X	X	X	X	X	X	X	X	X	X	IMP
Biological Process	GO:0017144	drug metabolic process	X	X	IDA	X	X	X	X	X	X	X	X	X
Biological Process	GO:0009790	embryonic development	X	X	IDA	X	X	X	X	X	X	X	X	X
Biological Process	GO:0007565	female pregnancy	X	X	IDA	X	X	X	X	X	X	X	X	X
Biological Process	GO:0031100	organ regeneration	X	X	IDA	X	X	X	X	X	X	X	X	X
Biological Process	GO:0014075	response to amine stimulus	X	X	IEP	X	X	X	X	X	X	X	X	X
Biological Process	GO:0031000	response to caffeine	X	X	IEP	X	X	X	X	X	X	X	X	X
Biological Process	GO:0033574	response to testosterone stimulus	X	X	IEP	X	X	X	X	X	X	X	X	X
Biological Process	GO:0046132	pyrimidine ribonucleoside biosynthetic process	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0009792	embryonic development ending in birth or egg hatching	X	X	X	X	X	X	IMP IGI	X	X	X	X	X
Biological Process	GO:0048562	embryonic organ morphogenesis	X	X	X	X	X	X	IMP IGI	X	X	X	X	X
Biological Process	GO:0035121	tail morphogenesis	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0040010	positive regulation of growth rate	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0018991	oviposition	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0050891	multicellular organismal water homeostasis	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0002119	nematode larval development	X	X	X	X	X	X	IMP IGI	X	X	X	X	X
Biological Process	GO:0060323	head morphogenesis	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0030036	actin cytoskeleton organization	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0045104	intermediate filament cytoskeleton organization	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0015012	heparan sulfate proteoglycan biosynthetic process	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0050654	chondroitin sulfate proteoglycan metabolic process	X	X	X	X	X	X	IMP	X	X	X	X	X
Biological Process	GO:0006526	arginine biosynthetic process	X	X	X	X	X	X	X	X	X	X	X	IMP
Cellular Component	GO:0005829	cytosol	IDA	ISS	X	X	X	X	X	X	X	X	X	X
Cellular Component	GO:0005634	nucleus	IDA	ISS	X	X	X	X	X	X	X	X	X	X
Cellular Component	GO:0016363	nuclear matrix	IDA	X	X	X	X	X	X	X	X	X	X	X
Cellular Component	GO:0005737	cytoplasm	X	ISS	X	X	X	X	X	X	X	X	X	IDA
Cellular Component	GO:0043234	protein complex	X	X	IDA	X	X	IDA	X	X	X	X	X	X
Cellular Component	GO:0005625	soluble fraction	X	X	IDA	X	X	X	X	X	X	X	X	X

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Group	Organism	Gene	Qualifier	GO ID	GO term name	Reference(s)	Evidence Code	with/from	Aspect	Notes	Status
FlyBase	Drosophila	r		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:4218218^[1]	IMP: Inferred from Mutant Phenotype		F		complete
FlyBase	Drosophila	r		GO:0004070	aspartate carbamoyltransferase activity	PMID:4218218^[1]	IMP: Inferred from Mutant Phenotype		F		complete
FlyBase	Drosophila	r		GO:0006207	'de novo' pyrimidine base biosynthetic process	PMID:4218218^[1]	IMP: Inferred from Mutant Phenotype		P		complete
GOA	Human	CAD		GO:0019899	enzyme binding	PMID:15326225^[2]	IPI	Q99638	F		complete
BHF-UCL	Human	CAD		GO:0005829	cytosol	PMID:15890648^[3]	IDA		C		complete
BHF-UCL	Human	CAD		GO:0005634	nucleus	PMID:15890648^[3]	IDA		C		complete
BHF-UCL	Human	CAD		GO:0016363	nuclear matrix	PMID:9525610^[4]	IDA		C		complete
BHF-UCL	Human	CAD		GO:0018107	peptidyl-threonine phosphorylation	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	P08955	P	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0046777	protein amino acid autophosphorylation	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	P08955	P	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0006207	'de novo' pyrimidine base biosynthetic process	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	P08955	P	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0004070	aspartate carbamoyltransferase activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	P08955	F	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0005524	ATP binding	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	P08955	F	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0016597	amino acid binding	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	P08955	F	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	P08955	F	ISS from hamster protein	complete
BHF-UCL	Human	CAD		GO:0004151	dihydroorotase activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	P08955	F	ISS from hamster protein	complete
FlyBase	Drosophila	r		GO:0004151	dihydroorotase activity	PMID:806025^[7]	IMP: Inferred from Mutant Phenotype		F		complete
FlyBase	Drosophila	r		GO:0004070	aspartate carbamoyltransferase activity	PMID:806025^[7]	IMP: Inferred from Mutant Phenotype		F		complete
FlyBase	Drosophila	r		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	BIOSIS:11600041556	IDA: Inferred from Direct Assay		F		complete
FlyBase	Drosophila	r		GO:0016597	amino acid binding	BIOSIS:11600041556	IC: Inferred by Curator	GO:0004088	F	Or IDA? NTR: glutamine binding?	complete
FlyBase	Drosophila	r		GO:0005524	ATP binding	BIOSIS:11600041556	IC: Inferred by Curator	GO:0004088	F	Or IDA?	complete
FlyBase	Drosophila	r		GO:0006541	glutamine metabolic process	BIOSIS:11600041556	IC: Inferred by Curator	GO:0004088	P	Or IDA? What happens to glutamine in reaction is not measured.	complete
EcoliWiki	E. coli	CarB		GO:0005524	ATP binding	PMID:14718657^[8]	IMP: Inferred from Mutant Phenotype		F	Compared carbamoyl phosphate synthetase activity for wild-type and mutants in ATP-binding domain.	complete
EcoliWiki	E. coli	CarB	Contributes to	GO:0004086	carbamoyl-phosphate synthase activity	PMID:14718657^[8]	IDA: Inferred from Direct Assay		F	CarAB was assayed for glutamine-dependent carbamoyl phosphate synthetase activity in a coupled assay.	complete
EcoliWiki	E. coli	CarB		GO:0005515	protein binding	PMID:4358555^[9]	IDA: Inferred from Direct Assay		F	CarA (light subunit) and CarB (heavy subunit) were reversibly separated using gel filtration.	complete
EcoliWiki	E. coli	CarB		GO:0004086	carbamoyl-phosphate synthase activity	PMID:3549732^[10]	IDA: Inferred from Direct Assay		F	Purified CarB was assayed for carbamoyl phosphate synthetase activity and compared to the holoenzyme (consisting of CarA and CarB).	complete
EcoliWiki	E. coli	CarB		GO:0046872	metal ion binding	PMID:229896^[11]	IDA: Inferred from Direct Assay		F	Carbamoyl phosphate synthetase activity was assayed in the absence (resulting in no activity) or presence of varying concentrations of divalent cations (Mg2+, Ca2+, Mg2+, Co2+, or Zn2+).	complete
EcoliWiki	E. coli	CarB		GO:0000166	nucleotide binding	PMID:10843852^[12]	IMP: Inferred from Mutant Phenotype		F	Carbamoyl phosphate synthetase activity of wild-type and mutant proteins was monitored in the presence of varying concentrations of ornithine, IMP and UMP.	complete
EcoliWiki	E. coli	CarB		GO:0019856	pyrimidine base biosynthetic process	PMID:1737023^[13]	IMP: Inferred from Mutant Phenotype		P	E. coli mutants were isolated that were auxotrophic for arginine and uracil and the mutations were shown to be located in the carB gene.	complete
EcoliWiki	E. coli	CarB		GO:0008652	amino acid biosynthetic process	PMID:1737023^[13]	IMP: Inferred from Mutant Phenotype		P	E. coli mutants were isolated that were auxotrophic for arginine and uracil and the mutations were shown to be located in the carB gene.	complete
EcoliWiki	E. coli	CarB		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:1737023^[13]	IGI: Inferred from Genetic Interaction	EcoliWiki:carA	F	CarB mutants are unable to use ammonia or glutamine as the nitrogen donor for carbamoyl phosphate synthesis.	complete
MGI	Mouse	Cad		GO:0005737	cytoplasm	PMID:15890648^[3]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	C	ISO mouse orthology to hamster Based more on the immunohistochem than the fractionation.	complete
MGI	Mouse	Cad		GO:0005634	nucleus	PMID:15890648^[3]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	C	ISO modification:MOD:00047; O-phospho-L-threonine\|thr456 Phosphorylated form is nuclear	complete
MGI	Mouse	Cad		GO:0005524	ATP binding	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO orthology to hamster	complete
MGI	Mouse	Cad		GO:0004070	aspartate carbamoyltransferase activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO to hamster	complete
MGI	Mouse	Cad		GO:0004151	dihydroorotase activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO hamster	complete
MGI	Mouse	Cad		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO hamster	complete
MGI	Mouse	Cad		GO:0004672	protein kinase activity	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO hamster target:P08955\|thr1037	complete
MGI	Mouse	Cad		GO:0006207	'de novo' pyrimidine base biosynthetic process	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	P	ISO to hamster IC\|GO:0004070\|GO:0004088\|GO:0004151	complete
MGI	Mouse	Cad		GO:0046777	protein amino acid autophosphorylation	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	P	ISO hamster target:P08955\|thr1037	complete
MGI	Mouse	Cad		GO:0018107	peptidyl-threonine phosphorylation	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	P	ISO hamster target:P08955\|thr1037	complete
RGD	Rat	Cad		GO:0004070	aspartate carbamoyltransferase activity	PMID:1148171^[14]	IDA: Inferred from Direct Assay		F		complete
MGI	Mouse	Cad		GO:0004070	aspartate carbamoyltransferase activity	PMID:19472^[6]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	ISO hamster	complete
RGD	Rat	Cad		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:1148171^[14]	IDA: Inferred from Direct Assay		F		complete
RGD	Rat	Cad		GO:0004151	dihydroorotase activity	PMID:1148171^[14]	IDA: Inferred from Direct Assay		F		complete
RGD	Rat	Cad		GO:0042802	identical protein binding	PMID:26565^[15]	IDA: Inferred from Direct Assay		F		complete
RGD	Rat	Cad		GO:0043234	protein complex	PMID:26565^[15]	IDA: Inferred from Direct Assay		C		complete
RGD	Rat	Cad		GO:0005625	soluble fraction	PMID:12803^[16]	IDA: Inferred from Direct Assay		C		complete
RGD	Rat	Cad		GO:0017144	drug metabolic process	PMID:18515330^[17]	IDA: Inferred from Direct Assay		P		complete
RGD	Rat	Cad		GO:0009790	embryonic development	PMID:14160653^[18]	IDA: Inferred from Direct Assay		P		complete
RGD	Rat	Cad		GO:0007565	female pregnancy	PMID:6020217^[19]	IDA: Inferred from Direct Assay		P		complete
RGD	Rat	Cad		GO:0031100	organ regeneration	PMID:13671431^[20]	IDA: Inferred from Direct Assay		P		complete
RGD	Rat	Cad		GO:0014075	response to amine stimulus	PMID:2864015^[21]	IEP: Inferred from Expression Pattern		P		complete
RGD	Rat	Cad		GO:0031000	response to caffeine	PMID:6149265^[22]	IEP: Inferred from Expression Pattern		P		complete
RGD	Rat	Cad		GO:0033574	response to testosterone stimulus	PMID:6030068^[23]	IEP: Inferred from Expression Pattern		P		complete
MGI	Mouse	Cad		GO:0002134	UTP binding	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	F	New term: UTP binding ISO to hamster Based on assays of UTP allosteric inhibition of phosphorylated and non-phosphorylated species.	complete
MGI	Mouse	Cad		GO:0005829	cytosol	PMID:11986331^[5]	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P08955	C	orthology to hamster. included for completeness. Term as used by them is more of a "fraction"	complete
FlyBase	Drosophila	r		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:28118^[24]	IDA: Inferred from Direct Assay		F		complete
FlyBase	Drosophila	r		GO:0043234	protein complex	PMID:28118^[24]	IDA: Inferred from Direct Assay		C		complete
FlyBase	Drosophila	r		GO:0004151	dihydroorotase activity	PMID:28118^[24]	IDA: Inferred from Direct Assay		F		complete
FlyBase	Drosophila	r		GO:0004070	aspartate carbamoyltransferase activity	PMID:28118^[24]	IDA: Inferred from Direct Assay		F		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0019856	pyrimidine base biosynthetic process	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
FlyBase	Drosophila	r		GO:0006207	'de novo' pyrimidine base biosynthetic process	PMID:5004701^[26]	IMP: Inferred from Mutant Phenotype		P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0046132	pyrimidine ribonucleoside biosynthetic process	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0009792	embryonic development ending in birth or egg hatching	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0009792	embryonic development ending in birth or egg hatching	PMID:16828468^[25]	IGI: Inferred from Genetic Interaction	WB:WBGene00004360	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0048562	embryonic organ morphogenesis	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0048562	embryonic organ morphogenesis	PMID:16828468^[25]	IGI: Inferred from Genetic Interaction	WB:WBGene00004360	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0035121	tail morphogenesis	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0040010	positive regulation of growth rate	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0018991	oviposition	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0050891	multicellular organismal water homeostasis	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0002119	nematode larval development	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype		P	Based on an RNAi experiment not yet annotated in WB.	complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0002119	nematode larval development	PMID:16828468^[25]	IGI: Inferred from Genetic Interaction	WB:WBGene00004360	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0060323	head morphogenesis	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype		P	Based on an RNAi experiment not yet curated in WB.	complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0030036	actin cytoskeleton organization	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0045104	intermediate filament cytoskeleton organization	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0015012	heparan sulfate proteoglycan biosynthetic process	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P		complete
WormBase	C.elegans	pyr-1 (WBGene00004259)		GO:0050654	chondroitin sulfate proteoglycan metabolic process	PMID:16828468^[25]	IMP: Inferred from Mutant Phenotype	WB:cu8	P	Chondroitin sulfate levels increase in pyr-1 mutant animals.	complete
DictyBase	Dicty	pyr1-3\|DDB_G0276335		GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:2568162^[27]	IDA: Inferred from Direct Assay		F		complete
DictyBase	Dicty	pyr1-3\|DDB_G0276335		GO:0004070	aspartate carbamoyltransferase activity	PMID:2568162^[27]	IDA: Inferred from Direct Assay		F		complete
DictyBase	Dicty	pyr1-3\|DDB_G0276335		GO:0004151	dihydroorotase activity	PMID:2568162^[27]	IDA: Inferred from Direct Assay		F		complete
DictyBase	Dicty	pyr1-3\|DDB_G0276335		GO:0006541	glutamine metabolic process	PMID:2568162^[27]	IDA: Inferred from Direct Assay		P		complete
EcoliWiki	E. coli	carA		GO:0005737	cytoplasm	PMID:2682645^[28]	IDA: Inferred from Direct Assay		C		complete
EcoliWiki	E. coli	carA		GO:0005515	protein binding	PMID:2682645^[28]	IMP: Inferred from Mutant Phenotype		F		complete
EcoliWiki	E. coli	carA		GO:0006541	glutamine metabolic process	PMID:1827118^[29]	IMP: Inferred from Mutant Phenotype		P		complete
EcoliWiki	E. coli	carA	Contributes to	GO:0004088	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	PMID:1827118^[29]	IMP: Inferred from Mutant Phenotype		F		complete
EcoliWiki	E. coli	carA		GO:0006207	'de novo' pyrimidine base biosynthetic process	PMID:5319709^[30]	IMP: Inferred from Mutant Phenotype		P		complete
EcoliWiki	E. coli	carA		GO:0006526	arginine biosynthetic process	PMID:5319709^[30]	IMP: Inferred from Mutant Phenotype		P		complete
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Notes

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Minutes

E. coli: CPS2 function annotation two genes, carA and carB, and it's complex, both annotated

Yes, annotate all here and choose what's used for propagation.

London: a term describing allosteric regulation would be useful. Allosteric (mechanics) are outside of GO scope, only the regulation part is important

Regulation discussion. What experiments needed to use regulation term?
Poll:

Would you annotate to both 'regulation of process x' and also to 'process x' for a key protein in the pathway which has also been found to regulate the whole pathway by its allosteric binding site

- 67% yes, 11% NO, 22% Unsure

References

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See Help:References for how to manage references in GONUTS.

↑ ^1.0 ^1.1 ^1.2 Norby S (1973) The biochemical genetics of rudimentary mutants of Drosophila melanogaster. I. Aspartate carbamoyltransferase levels in complementing and non-complementing strains. Hereditas 73: 11-6 PubMed GONUTS page
↑ Lindsey-Boltz LA et al. (2004) The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase activity of the multifunctional protein CAD. Nucleic Acids Res 32: 4524-30 PubMed GONUTS page
↑ ^3.0 ^3.1 ^3.2 ^3.3 Sigoillot FD et al. (2005) Nuclear localization and mitogen-activated protein kinase phosphorylation of the multifunctional protein CAD. J Biol Chem 280: 25611-20 PubMed GONUTS page
↑ Angeletti PC & Engler JA (1998) Adenovirus preterminal protein binds to the CAD enzyme at active sites of viral DNA replication on the nuclear matrix. J Virol 72: 2896-904 PubMed GONUTS page
↑ ^5.0 ^5.1 ^5.2 ^5.3 ^5.4 ^5.5 ^5.6 ^5.7 ^5.8 Sigoillot FD et al. (2002) Autophosphorylation of the mammalian multifunctional protein that initiates de novo pyrimidine biosynthesis. J Biol Chem 277: 24809-17 PubMed GONUTS page
↑ ^6.0 ^6.1 ^6.2 ^6.3 ^6.4 ^6.5 ^6.6 ^6.7 ^6.8 ^6.9 Coleman PF et al. (1977) Purification from hamster cells of the multifunctional protein that initiates de novo synthesis of pyrimidine nucleotides. J Biol Chem 252: 6379-85 PubMed GONUTS page
↑ ^7.0 ^7.1 Rawls JM & Fristrom JW (1975) A complex genetic locus that controls of the first three steps of pyrimidine biosynthesis in Drosophila. Nature 255: 738-40 PubMed GONUTS page
↑ ^8.0 ^8.1 Kothe M & Powers-Lee SG (2004) Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase. Protein Sci 13: 466-75 PubMed GONUTS page
↑ Trotta PP et al. (1974) Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits. J Biol Chem 249: 492-9 PubMed GONUTS page
↑ Rubino SD et al. (1987) In vivo synthesis of carbamyl phosphate from NH3 by the large subunit of Escherichia coli carbamyl phosphate synthetase. J Biol Chem 262: 4382-6 PubMed GONUTS page
↑ Raushel FM et al. (1979) Paramagnetic probes for carbamoyl-phosphate synthetase: metal ion binding studies and preparation of nitroxide spin-labeled derivatives. Biochemistry 18: 5562-6 PubMed GONUTS page
↑ Fresquet V et al. (2000) Site-directed mutagenesis of the regulatory domain of Escherichia coli carbamoyl phosphate synthetase identifies crucial residues for allosteric regulation and for transduction of the regulatory signals. J Mol Biol 299: 979-91 PubMed GONUTS page
↑ ^13.0 ^13.1 ^13.2 Guillou F et al. (1992) Mutational analysis of carbamyl phosphate synthetase. Substitution of Glu841 leads to loss of functional coupling between the two catalytic domains of the synthetase subunit. Biochemistry 31: 1656-64 PubMed GONUTS page
↑ ^14.0 ^14.1 ^14.2 Mori M et al. (1975) Aggregation states and catalytic properties of the multienzyme complex catalyzing the initial steps of pyrimidine biosynthesis in rat liver. Biochemistry 14: 2622-30 PubMed GONUTS page
↑ ^15.0 ^15.1 Mori M & Tatibana M (1978) Multi-enzyme complex of glutamine-dependent carbamoyl-phosphate synthetase with aspartate carbamoyltransferase and dihydroorotase from rat ascites-hepatoma cells. Purification, molecular properties and limited proteolysis. Eur J Biochem 86: 381-8 PubMed GONUTS page
↑ Bond JS (1976) Acid inactivation of short-lived rat liver enzymes. Biochim Biophys Acta 451: 238-49 PubMed GONUTS page
↑ Schroeder PE et al. (2008) The dihydroorotase inhibitor 5-aminoorotic acid inhibits the metabolism in the rat of the cardioprotective drug dexrazoxane and its one-ring open metabolites. Drug Metab Dispos 36: 1780-5 PubMed GONUTS page
↑ NORDMANN Y et al. (1964) ACTIVITY OF ASPARTATE TRANSCARBAMYLASE IN HEART AND LIVER OF THE DEVELOPING RAT. Nature 201: 616-7 PubMed GONUTS page
↑ Thibodeau PS & Thayer SA (1967) Effect of pregnancy and hormones on the activity of aspartate transcarbamylase and the level of nucleic acids in the mammary gland of the rat. Endocrinology 80: 505-9 PubMed GONUTS page
↑ CALVA E & COHEN PP (1959) Carbamyl phosphate-aspartate transcarbamylase activity in regenerating rat liver. Cancer Res 19: 679-83 PubMed GONUTS page
↑ Karsai T et al. (1985) Effect of dimethylnitrosamine upon carbamoyl phosphate and ornithine utilization in rat liver. Anticancer Res 5: 441-4 PubMed GONUTS page
↑ Miñana MD et al. (1984) Lesch-Nyhan syndrome, caffeine model: increase of purine and pyrimidine enzymes in rat brain. J Neurochem 43: 1556-60 PubMed GONUTS page
↑ Görlich M & Heise E (1967) Activity of aspartate transcarbamylase in mammary tumours induced by 7,12-dimethyl-benzanthracene in the rat. Nature 213: 934-5 PubMed GONUTS page
↑ ^24.0 ^24.1 ^24.2 ^24.3 Brothers VM et al. (1978) Rudimentary locus of Drosophila melanogaster: partial purification of a carbamylphosphate synthase--aspartate transcarbamylase--dihydroorotase complex. Biochem Genet 16: 321-32 PubMed GONUTS page
↑ ^25.00 ^25.01 ^25.02 ^25.03 ^25.04 ^25.05 ^25.06 ^25.07 ^25.08 ^25.09 ^25.10 ^25.11 ^25.12 ^25.13 ^25.14 ^25.15 ^25.16 Franks DM et al. (2006) C. elegans pharyngeal morphogenesis requires both de novo synthesis of pyrimidines and synthesis of heparan sulfate proteoglycans. Dev Biol 296: 409-20 PubMed GONUTS page
↑ Norby S (1970) A specific nutritional requirement for pyrimidines in rudimentary mutants of Drosophila melanogaster. Hereditas 66: 205-14 PubMed GONUTS page
↑ ^27.0 ^27.1 ^27.2 ^27.3 Wales ME et al. (1989) Characterization of pyrimidine metabolism in the cellular slime mold, Dictyostelium discoideum. Can J Microbiol 35: 432-8 PubMed GONUTS page
↑ ^28.0 ^28.1 Guillou F et al. (1989) Escherichia coli carbamoyl-phosphate synthetase: domains of glutaminase and synthetase subunit interaction. Proc Natl Acad Sci U S A 86: 8304-8 PubMed GONUTS page
↑ ^29.0 ^29.1 Mullins LS et al. (1991) Alterations in the energetics of the carbamoyl phosphate synthetase reaction by site-directed modification of the essential sulfhydryl group. J Biol Chem 266: 8236-40 PubMed GONUTS page
↑ ^30.0 ^30.1 Piérard A & Wiame JM (1964) Regulation and mutation affecting a glutamine dependent formation of carbamyl phosphate in Escherichia coli. Biochem Biophys Res Commun 15: 76-81 PubMed GONUTS page

[PMID:4218218-0] 1.0 ^1.1 ^1.2 Norby S (1973) The biochemical genetics of rudimentary mutants of Drosophila melanogaster. I. Aspartate carbamoyltransferase levels in complementing and non-complementing strains. Hereditas 73: 11-6 PubMed GONUTS page

[PMID:15326225-1] Lindsey-Boltz LA et al. (2004) The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase activity of the multifunctional protein CAD. Nucleic Acids Res 32: 4524-30 PubMed GONUTS page

[PMID:15890648-2] 3.0 ^3.1 ^3.2 ^3.3 Sigoillot FD et al. (2005) Nuclear localization and mitogen-activated protein kinase phosphorylation of the multifunctional protein CAD. J Biol Chem 280: 25611-20 PubMed GONUTS page

[PMID:9525610-3] Angeletti PC & Engler JA (1998) Adenovirus preterminal protein binds to the CAD enzyme at active sites of viral DNA replication on the nuclear matrix. J Virol 72: 2896-904 PubMed GONUTS page

[PMID:11986331-4] 5.0 ^5.1 ^5.2 ^5.3 ^5.4 ^5.5 ^5.6 ^5.7 ^5.8 Sigoillot FD et al. (2002) Autophosphorylation of the mammalian multifunctional protein that initiates de novo pyrimidine biosynthesis. J Biol Chem 277: 24809-17 PubMed GONUTS page

[PMID:19472-5] 6.0 ^6.1 ^6.2 ^6.3 ^6.4 ^6.5 ^6.6 ^6.7 ^6.8 ^6.9 Coleman PF et al. (1977) Purification from hamster cells of the multifunctional protein that initiates de novo synthesis of pyrimidine nucleotides. J Biol Chem 252: 6379-85 PubMed GONUTS page

[PMID:806025-6] 7.0 ^7.1 Rawls JM & Fristrom JW (1975) A complex genetic locus that controls of the first three steps of pyrimidine biosynthesis in Drosophila. Nature 255: 738-40 PubMed GONUTS page

[PMID:14718657-7] 8.0 ^8.1 Kothe M & Powers-Lee SG (2004) Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase. Protein Sci 13: 466-75 PubMed GONUTS page

[PMID:4358555-8] Trotta PP et al. (1974) Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits. J Biol Chem 249: 492-9 PubMed GONUTS page

[PMID:3549732-9] Rubino SD et al. (1987) In vivo synthesis of carbamyl phosphate from NH3 by the large subunit of Escherichia coli carbamyl phosphate synthetase. J Biol Chem 262: 4382-6 PubMed GONUTS page

[PMID:229896-10] Raushel FM et al. (1979) Paramagnetic probes for carbamoyl-phosphate synthetase: metal ion binding studies and preparation of nitroxide spin-labeled derivatives. Biochemistry 18: 5562-6 PubMed GONUTS page

[PMID:10843852-11] Fresquet V et al. (2000) Site-directed mutagenesis of the regulatory domain of Escherichia coli carbamoyl phosphate synthetase identifies crucial residues for allosteric regulation and for transduction of the regulatory signals. J Mol Biol 299: 979-91 PubMed GONUTS page

[PMID:1737023-12] 13.0 ^13.1 ^13.2 Guillou F et al. (1992) Mutational analysis of carbamyl phosphate synthetase. Substitution of Glu841 leads to loss of functional coupling between the two catalytic domains of the synthetase subunit. Biochemistry 31: 1656-64 PubMed GONUTS page

[PMID:1148171-13] 14.0 ^14.1 ^14.2 Mori M et al. (1975) Aggregation states and catalytic properties of the multienzyme complex catalyzing the initial steps of pyrimidine biosynthesis in rat liver. Biochemistry 14: 2622-30 PubMed GONUTS page

[PMID:26565-14] 15.0 ^15.1 Mori M & Tatibana M (1978) Multi-enzyme complex of glutamine-dependent carbamoyl-phosphate synthetase with aspartate carbamoyltransferase and dihydroorotase from rat ascites-hepatoma cells. Purification, molecular properties and limited proteolysis. Eur J Biochem 86: 381-8 PubMed GONUTS page

[PMID:12803-15] Bond JS (1976) Acid inactivation of short-lived rat liver enzymes. Biochim Biophys Acta 451: 238-49 PubMed GONUTS page

[PMID:18515330-16] Schroeder PE et al. (2008) The dihydroorotase inhibitor 5-aminoorotic acid inhibits the metabolism in the rat of the cardioprotective drug dexrazoxane and its one-ring open metabolites. Drug Metab Dispos 36: 1780-5 PubMed GONUTS page

[PMID:14160653-17] NORDMANN Y et al. (1964) ACTIVITY OF ASPARTATE TRANSCARBAMYLASE IN HEART AND LIVER OF THE DEVELOPING RAT. Nature 201: 616-7 PubMed GONUTS page

[PMID:6020217-18] Thibodeau PS & Thayer SA (1967) Effect of pregnancy and hormones on the activity of aspartate transcarbamylase and the level of nucleic acids in the mammary gland of the rat. Endocrinology 80: 505-9 PubMed GONUTS page

[PMID:13671431-19] CALVA E & COHEN PP (1959) Carbamyl phosphate-aspartate transcarbamylase activity in regenerating rat liver. Cancer Res 19: 679-83 PubMed GONUTS page

[PMID:2864015-20] Karsai T et al. (1985) Effect of dimethylnitrosamine upon carbamoyl phosphate and ornithine utilization in rat liver. Anticancer Res 5: 441-4 PubMed GONUTS page

[PMID:6149265-21] Miñana MD et al. (1984) Lesch-Nyhan syndrome, caffeine model: increase of purine and pyrimidine enzymes in rat brain. J Neurochem 43: 1556-60 PubMed GONUTS page

[PMID:6030068-22] Görlich M & Heise E (1967) Activity of aspartate transcarbamylase in mammary tumours induced by 7,12-dimethyl-benzanthracene in the rat. Nature 213: 934-5 PubMed GONUTS page

[PMID:28118-23] 24.0 ^24.1 ^24.2 ^24.3 Brothers VM et al. (1978) Rudimentary locus of Drosophila melanogaster: partial purification of a carbamylphosphate synthase--aspartate transcarbamylase--dihydroorotase complex. Biochem Genet 16: 321-32 PubMed GONUTS page

[PMID:16828468-24] 25.00 ^25.01 ^25.02 ^25.03 ^25.04 ^25.05 ^25.06 ^25.07 ^25.08 ^25.09 ^25.10 ^25.11 ^25.12 ^25.13 ^25.14 ^25.15 ^25.16 Franks DM et al. (2006) C. elegans pharyngeal morphogenesis requires both de novo synthesis of pyrimidines and synthesis of heparan sulfate proteoglycans. Dev Biol 296: 409-20 PubMed GONUTS page

[PMID:5004701-25] Norby S (1970) A specific nutritional requirement for pyrimidines in rudimentary mutants of Drosophila melanogaster. Hereditas 66: 205-14 PubMed GONUTS page

[PMID:2568162-26] 27.0 ^27.1 ^27.2 ^27.3 Wales ME et al. (1989) Characterization of pyrimidine metabolism in the cellular slime mold, Dictyostelium discoideum. Can J Microbiol 35: 432-8 PubMed GONUTS page

[PMID:2682645-27] 28.0 ^28.1 Guillou F et al. (1989) Escherichia coli carbamoyl-phosphate synthetase: domains of glutaminase and synthetase subunit interaction. Proc Natl Acad Sci U S A 86: 8304-8 PubMed GONUTS page

[PMID:1827118-28] 29.0 ^29.1 Mullins LS et al. (1991) Alterations in the energetics of the carbamoyl phosphate synthetase reaction by site-directed modification of the essential sulfhydryl group. J Biol Chem 266: 8236-40 PubMed GONUTS page

[PMID:5319709-29] 30.0 ^30.1 Piérard A & Wiame JM (1964) Regulation and mutation affecting a glutamine dependent formation of carbamyl phosphate in Escherichia coli. Biochem Biophys Res Commun 15: 76-81 PubMed GONUTS page

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RefGenome Electronic Jamboree 2009-02 CAD

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