Reviewed, UniProtKB/Swiss-Prot P0A6F1 (CARA_ECOLI)

Names and origin

Protein names

Recommended name:
    Carbamoyl-phosphate synthase small chain
    EC=6.3.5.5
Alternative name(s):
    Carbamoyl-phosphate synthetase glutamine chain

Gene names

Name:	carA
Synonyms:	pyrA
Ordered Locus Names:	b0032, JW0030

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	382 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate. HAMAP MF_01209
Pathway	Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl phosphate from bicarbonate: step 1/1. HAMAP MF_01209 Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. HAMAP MF_01209
Subunit structure	Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Tetramer of heterodimers (alpha,beta)4. HAMAP MF_01209
Sequence similarities	Belongs to the carA family. Contains 1 glutamine amidotransferase type-1 domain.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Arginine biosynthesis Pyrimidine biosynthesis
Domain	Glutamine amidotransferase
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from mutant phenotype. Source: UniProtKB arginine biosynthetic process Inferred from mutant phenotype. Source: UniProtKB glutamine metabolic process Inferred from mutant phenotype. Source: UniProtKB pyrimidine nucleotide biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
carB	P00968	2	EBI-546107,EBI-546118
murE	P22188	1	EBI-546107,EBI-553061
yggM	P46142	1	EBI-546107,EBI-1125200

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 382

382

Carbamoyl-phosphate synthase small chain HAMAP MF_01209

PRO_0000112274

Regions

Domain

193 – 380

188

Glutamine amidotransferase type-1

Region

1 – 189

189

CPSase HAMAP MF_01209

Sites

Active site

269

1

Nucleophile By similarity

Active site

353

1

By similarity

Active site

355

1

By similarity

Secondary structure

1

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382

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Beta strand

14 – 19

6

Beta strand

23 – 33

11

Helix

39 – 43

5

Helix

46 – 48

3

Beta strand

51 – 55

5

Beta strand

57 – 59

3

Helix

67 – 69

3

Beta strand

71 – 74

4

Beta strand

77 – 81

5

Helix

98 – 104

7

Beta strand

108 – 113

6

Helix

115 – 125

11

Beta strand

128 – 137

10

Helix

140 – 149

10

Helix

159 – 162

4

Beta strand

168 – 170

3

Turn

177 – 179

3

Helix

187 – 189

3

Beta strand

192 – 200

9

Helix

203 – 211

9

Beta strand

214 – 220

7

Helix

225 – 229

5

Beta strand

234 – 238

5

Helix

249 – 258

10

Beta strand

265 – 268

4

Helix

270 – 278

9

Beta strand

283 – 299

17

Turn

300 – 303

4

Beta strand

304 – 316

13

Beta strand

325 – 331

7

Turn

332 – 334

3

Beta strand

337 – 352

16

Beta strand

357 – 359

3

Turn

362 – 364

3

Helix

365 – 379

15

Sequences

	Sequence		Length	Mass (Da)
	P0A6F1-1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 60BC26366417443F	FASTA	382	41,431
	10 20 30 40 50 60 MIKSALLVLE DGTQFHGRAI GATGSAVGEV VFNTSMTGYQ EILTDPSYSR QIVTLTYPHI 70 80 90 100 110 120 GNVGTNDADE ESSQVHAQGL VIRDLPLIAS NFRNTEDLSS YLKRHNIVAI ADIDTRKLTR 130 140 150 160 170 180 LLREKGAQNG CIIAGDNPDA ALALEKARAF PGLNGMDLAK EVTTAEAYSW TQGSWTLTGG 190 200 210 220 230 240 LPEAKKEDEL PFHVVAYDFG AKRNILRMLV DRGCRLTIVP AQTSAEDVLK MNPDGIFLSN 250 260 270 280 290 300 GPGDPAPCDY AITAIQKFLE TDIPVFGICL GHQLLALASG AKTVKMKFGH HGGNHPVKDV 310 320 330 340 350 360 EKNVVMITAQ NHGFAVDEAT LPANLRVTHK SLFDGTLQGI HRTDKPAFSF QGHPEASPGP 370 380 HDAAPLFDHF IELIEQYRKT AK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence of the carA gene and the control region of carAB: tandem promoters, respectively controlled by arginine and the pyrimidines, regulate the synthesis of carbamoyl-phosphate synthetase in Escherichia coli K-12." Piette J., Nyunoya H., Lusty C.J., Cunin R., Weyens G., Crabeel M., Charlier D.R.M., Glansdorff N., Pierard A. Proc. Natl. Acad. Sci. U.S.A. 81:4134-4138(1984) [PubMed: 6330744] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Multiple regulatory signals in the control region of the Escherichia coli carAB operon." Bouvier J., Patte J.-C., Stragier P. Proc. Natl. Acad. Sci. U.S.A. 81:4139-4143(1984) [PubMed: 6377309] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase." Nyunoya H., Lusty C.J. Proc. Natl. Acad. Sci. U.S.A. 80:4629-4633(1983) [PubMed: 6308632] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 361-382.
[7]	"A whole genome approach to in vivo DNA-protein interactions in E. coli." Wang M.X., Church G.M. Nature 360:606-610(1992) [PubMed: 1334233] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16. Strain: K12.
[8]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[9]	"Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product." Thoden J.B., Holden H.M., Wesenberg G., Raushel F.M., Rayment I. Biochemistry 36:6305-6316(1997) [PubMed: 9174345] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[10]	"Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis." Thoden J.B., Miran S.G., Phillips J.C., Howard A.J., Raushel F.M., Holden H.M. Biochemistry 37:8825-8831(1998) [PubMed: 9636022] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[11]	"The structure of carbamoyl phosphate synthetase determined to 2.1-A resolution." Thoden J.B., Raushel F.M., Benning M.M., Rayment I., Holden H.M. Acta Crystallogr. D 55:8-24(1999) [PubMed: 10089390] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[12]	"Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding." Thoden J.B., Wesenberg G., Raushel F.M., Holden H.M. Biochemistry 38:2347-2357(1999) [PubMed: 10029528] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[13]	"The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway." Thoden J.B., Huang X., Raushel F.M., Holden H.M. Biochemistry 38:16158-16166(1999) [PubMed: 10587438] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[14]	"The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase." Thoden J.B., Raushel F.M., Wesenberg G., Holden H.M. J. Biol. Chem. 274:22502-22507(1999) [PubMed: 10428826] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01597 Genomic DNA. Translation: AAA23538.1.
U00096 Genomic DNA. Translation: AAC73143.1.
AP009048 Genomic DNA. Translation: BAB96601.1.
X70017 Genomic DNA. Translation: CAA49615.1.

PIR

SYECCS. A01128.
B85484.

RefSeq

AP_000696.1.
NP_414573.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A9X	X-ray	1.80	B/D/F/H	2-380	[»]
1BXR	X-ray	2.10	B/D/F/H	1-382	[»]
1C30	X-ray	2.00	B/D/F/H	1-382	[»]
1C3O	X-ray	2.10	B/D/F/H	1-382	[»]
1CE8	X-ray	2.10	B/D/F/H	1-382	[»]
1CS0	X-ray	2.00	B/D/F/H	1-382	[»]
1JDB	X-ray	2.10	C/F/I/L	1-382	[»]
1KEE	X-ray	2.10	B/D/F/H	1-382	[»]
1M6V	X-ray	2.10	B/D/F/H	1-382	[»]
1T36	X-ray	2.10	B/D/F/H	1-382	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A6F1. 14 interactions.

STRING

P0A6F1.

2-D gel databases

SWISS-2DPAGE

P0A6F1.

ECO2DBASE

G041.4. 6TH EDITION.

Genome annotation databases

GeneID

949025.

GenomeReviews

Gene locus JW0030 in contig AP009048_GR.
Gene locus b0032 in contig U00096_GR.

KEGG

ecj:JW0030.
eco:b0032.

Organism-specific databases

EchoBASE

EB0132.

EcoGene

EG10134. carA.

CMR

Search...

Phylogenomic databases

eggNOG

COG0505.

HOGENOM

HBG286341.

OMA

FTYPELG.

Enzyme and pathway databases

BioCyc

EcoCyc:CARBPSYN-SMALL.
ECOL168927:B0032-MONOMER.
MetaCyc:CARBPSYN-SMALL.

Gene expression databases

Genevestigator

P0A6F1.

Family and domain databases

HAMAP

MF_01209_B. CPSase_S_chain_B.
[Tree]

InterPro

IPR006220. Anth_synthII.
IPR001317. CarbamoylP_synth_GATase_dom.
IPR006274. CarbamoylP_synth_ssu.
IPR002474. CarbamoylP_synth_ssu_N.
IPR011702. GATASE.
IPR017926. GATASE_1.
IPR000991. GATase_class1_C.
[Graphical view]

PANTHER

PTHR11405:SF4. CarA_synth_small. 1 hit.

Pfam

PF00988. CPSase_sm_chain. 1 hit.
PF00117. GATase. 1 hit.
[Graphical view]

PRINTS

PR00097. ANTSNTHASEII.
PR00099. CPSGATASE.
PR00096. GATASE.

TIGRFAMs

TIGR01368. CPSaseIIsmall. 1 hit.

PROSITE

PS51273. GATASE_TYPE_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CARA_ECOLI

Accession

Primary (citable) accession number: P0A6F1
Secondary accession number(s): P00907

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	February 9, 2010
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)