Escherichia coli K-12 substr. MG1655 Polypeptide: carbamoyl phosphate synthetase, β chain

Gene: carB Accession Numbers: EG10135 (EcoCyc), b0033, ECK0034

Synonyms: cap, pyrA, β chain, large chain

Regulation Summary Diagram: ?

Regulation summary diagram for carB

Component of: carbamoyl phosphate synthetase (extended summary available)

In E. coli, the large subunit encoded by carB gene is the synthetase component of the enzyme. It binds the two required molecules of MgATP and catalyzes the two required phosphorylation events. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain [Thoden99]. The large subunit alone can catalyze carbamyl phosphate synthesis from ammonia, but not from glutamine [Rubino87]. It uses NH3 and HCO3- in an ATP-dependent reaction to form carbamoyl phosphate [Guillou89]. This subunit has two catalytic nucleotide-binding domains, one involved in the activation of HCO3- and the second in phosphorylation of carbamate. Glu841 is an essential residue for the phosphorylation of carbamate in the terminal step of the catalytic mechanism [Guillou92].

Gene Citations: [Gigot80, Crabeel80, Shimada07]

Locations: cytosol

Map Position: [30,817 -> 34,038] (0.66 centisomes, 2°)
Length: 3222 bp / 1073 aa

Molecular Weight of Polypeptide: 117.84 kD (from nucleotide sequence)

pI: 5.43

Isozyme Sequence Similarity [Comment 1]:

Unification Links: ASAP:ABE-0000121 , CGSC:935 , DIP:DIP-1025N , EchoBASE:EB0133 , EcoGene:EG10135 , EcoliWiki:b0033 , Entrez-gene:944775 , Mint:MINT-1255866 , ModBase:P00968 , OU-Microarray:b0033 , PortEco:carB , PR:PRO_000022248 , Pride:P00968 , Protein Model Portal:P00968 , RefSeq:NP_414574 , RegulonDB:EG10135 , SMR:P00968 , String:511145.b0033 , UniProt:P00968

Relationship Links: InterPro:IN-FAMILY:IPR005479 , InterPro:IN-FAMILY:IPR005480 , InterPro:IN-FAMILY:IPR005481 , InterPro:IN-FAMILY:IPR005483 , InterPro:IN-FAMILY:IPR006275 , InterPro:IN-FAMILY:IPR011607 , InterPro:IN-FAMILY:IPR011761 , InterPro:IN-FAMILY:IPR013815 , InterPro:IN-FAMILY:IPR013816 , InterPro:IN-FAMILY:IPR016185 , PDB:Structure:1A9X , PDB:Structure:1BXR , PDB:Structure:1C30 , PDB:Structure:1C3O , PDB:Structure:1CE8 , PDB:Structure:1CS0 , PDB:Structure:1JDB , PDB:Structure:1KEE , PDB:Structure:1M6V , PDB:Structure:1T36 , Pfam:IN-FAMILY:PF00289 , Pfam:IN-FAMILY:PF02142 , Pfam:IN-FAMILY:PF02786 , Pfam:IN-FAMILY:PF02787 , Prints:IN-FAMILY:PR00098 , Prosite:IN-FAMILY:PS00866 , Prosite:IN-FAMILY:PS00867 , Prosite:IN-FAMILY:PS50975 , Smart:IN-FAMILY:SM00851 , Smart:IN-FAMILY:SM01096

In Paralogous Gene Group: 10 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for carB

GO Terms:

Biological Process: GO:0008652 - cellular amino acid biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Guillou92]
GO:0019856 - pyrimidine nucleobase biosynthetic process Inferred from experiment [Guillou92]
GO:0042710 - biofilm formation Inferred from experiment [Garavaglia12]
GO:0000050 - urea cycle Inferred by computational analysis [Gaudet10]
GO:0006221 - pyrimidine nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0006526 - arginine biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, Gaudet10]
GO:0006807 - nitrogen compound metabolic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0044205 - 'de novo' UMP biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0000166 - nucleotide binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Mareya95, Fresquet00]
GO:0004087 - carbamoyl-phosphate synthase (ammonia) activity Inferred from experiment [Rubino87]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Marsh13, Thoden98, Thoden99b, Thoden99a, Thoden02, Butland05]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Guillou92, Kothe04]
GO:0016597 - amino acid binding Inferred from experiment [Mareya95]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Raushel79]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004088 - carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity Inferred by computational analysis [GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005951 - carbamoyl-phosphate synthase complex Inferred from experiment [Trotta74]
GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids arginine
metabolism biosynthesis of building blocks nucleotides pyrimidine biosynthesis

Essentiality data for carB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 4]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose No 37 Aerobic 7.2 0.22 No [Baba06, Comment 3]
No [Feist07, Comment 5]

Subunit of: carbamoyl phosphate synthetase

Subunit composition of carbamoyl phosphate synthetase = [CarB]2[CarA]2
         carbamoyl phosphate synthetase, β chain = CarB (summary available)
         carbamoyl phosphate synthetase, α chain = CarA (summary available)

Carbamoyl phosphate synthetase from E. coli catalyzes the first committed step in the separate biosynthetic pathways for the production of arginine, and pyrimidine nucleotides. The enzyme is an α,β-heterodimer consisting of a small amidotransferase subunit complexed to a larger synthetase subunit. The small subunit, encoded by carA gene hydrolyzes glutamine to glutamate and ammonia. The large subunit, encoded by carB gene binds the two required molecules of MgATP and catalyzes the two required phosphorylation events. The small subunit contains a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain [Thoden99].

The enzyme contains a total of three separate active sites that are connected by an intramolecular tunnel. The small subunit harbors one of these active sites. Two molecular tunnels connect the three active sites contained within the small and large subunits. The ammonia tunnel extends from the active site of the small subunit to the active site of the carboxy phosphate domain of the large subunit. The carbamate tunnel connects the two active sites within the large subunit [Thoden04a].

The active sites of the enzyme are very resistant toward changes in nucleotide specificity, most likely owing to the presence of the K+-binding loop that prevents binding of GTP. Mutations at positions 144 and 690 interfere with access of substrate to the active sites [Kothe04].

Site directed mutagenesis showed that either a C269G or C269S mutation results in loss of all of the glutamine-dependent synthesis of carbamoylphosphate though the enzyme still retains the ability to use ammonia as the nitrogen source [Rubino87]. Mutagenesis of residues Glu783, Glu892 and Thr1042 that had been shown by crystallography to interact with bound ornithine demonstrated their importance for ornithine binding and provided insight into the mechanism of allosteric control of enzyme activity [Rochera02]. Site-directed mutagenesis studies also suggested that Cys269 and His353 of the conserved catalytic triad in the glutamine aminotransferase site may function as a catalytic dyad [Hart08]. The transfer of ammonia through the ammonia tunnel in this enzyme was investigated using a combination of molecular dynamics simulations and experimental characterization of mutations [Fan09]. This approach was also used to characterize the transport of carbamate through the large subunit of this enzyme [Lund10]. In another mutagenesis study, substiturion of six intrinsic tryptophan residues in the enzyme with tyrosine created a tryptophan-free variant. Subsequent substitutions of individual tryptophan residues at each site allowed their use as fluoresence probes to study conformational changes [Johnson07].

The large subunit contains the sites for the allosteric activators (NH4+, IMP, ornithine) and the inhibitor UMP [Trotta74]. Two residues, serine 948 and threonine 1042, appear crucial for allosteric regulation of the enzyme [Delannay99].

Last-Curated ? 30-Mar-2011 by Fulcher C , SRI International

Enzymatic reaction of: carbamoyl phosphate synthetase

Synonyms: carbamoyl-phosphate synthetase (glutamine-hydrolysing), glutamine-dependent carbamoyl-phosphate synthase, GD-CPSase, carbon-dioxide:L-glutamine amido-ligase (ADP-forming,carbamate-phosphorylating)

EC Number:

2 ATP + L-glutamine + hydrogen carbonate + H2O <=> carbamoyl-phosphate + L-glutamate + 2 ADP + phosphate + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: L-glutamine degradation I , superpathway of arginine and polyamine biosynthesis , superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis , superpathway of pyrimidine ribonucleotides de novo biosynthesis , L-arginine biosynthesis I (via L-ornithine) , UMP biosynthesis

The enzyme catalyzes the assembly of carbamoyl phosphate via a mechanism that requires at least four separate chemical reactions: phosphorylation of bicarbonate to carboxyphosphate; hydrolysis of glutamine to glutamate and ammonia; a nucleophilic attack of ammonia on carboxyphosphate yielding carbamate; and finally the phosphorylation of carbamate forming carbamoyl phosphate [Thoden99].

In addition to the Mg+2 needed to complex with the nucleotide substrate, free Mg+2 is an absolute requirement for activity. Other ions also bind at the divalent cation site and the nucleotide site [Raushel79].

In vitro the enzyme also catalyzed ATP synthesis from carbamoyl-phosphate and ADP in the reverse direction [Guillou92].

Cofactors or Prosthetic Groups: Mg2+ [Comment 6, Raushel79]

Alternative Cofactors for Mg2+: Mn2+ , Co2+ , Cd2+ , Zn2+

Activators (Allosteric): ammonium [Anderson77, Trotta74] , IMP [Anderson77, Trotta74] , L-ornithine [Anderson77, Trotta74]

Activators (Unknown Mechanism): K+ [Thoden99]

Inhibitors (Allosteric): UMP [Trotta74]

Inhibitors (Competitive): cyanate [Helmward89, Comment 7]

Inhibitors (Unknown Mechanism): acivicin [Helmward89] , 6-diazo-5-oxo-norvaline [Helmward89] , 6-diazo-5-oxonorleucine [Helmward89, Khedouri66] , L-azaserine [Helmward89, Khedouri66] , L-2-amino-4-oxo-5-chloropentanoate [Helmward89, Khedouri66]

Primary Physiological Regulators of Enzyme Activity: IMP , L-ornithine , UMP

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Lund10, BRENDA14]
[Kim04a, BRENDA14]
[Rishavy00, BRENDA14]
361.0, 890.0, 910.0, 1075.0, 1490.0, 1860.0
[Eroglu02, BRENDA14]
[Hart08, BRENDA14]
[SaeedKothe03, BRENDA14]
220.0, 320.0
[Yefimenko05, BRENDA14]
[Johnson07, BRENDA14]
51.0, 240.0
0.071, 0.015
[Lund10, BRENDA14]
5.0, 29.0
0.81, 0.14
[Kothe04, BRENDA14]
[Hart08, BRENDA14]
50.0, 60.0
2.2, 6.8
0.044, 0.14, 0.037, 0.11
[SaeedKothe03, BRENDA14]
430.0, 460.0
3.35, 8.0
0.0078, 0.019, 0.0073, 0.017
[Sahay98, BRENDA14]
hydrogen carbonate
1330.0, 1900.0
[Yefimenko05, BRENDA14]
hydrogen carbonate

pH(opt): 4.2 [BRENDA14, Rishavy00], 7.8 [BRENDA14, Meister89], 9.3 [BRENDA14, Rishavy00], 9.5 [BRENDA14, Meister89]

Sequence Features

Protein sequence of carbamoyl phosphate synthetase, beta chain with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Nyunoya83, UniProt11]
UniProt: Removed.
Protein-Segment 2 -> 403
UniProt: Carboxyphosphate synthetic domain; Sequence Annotation Type: region of interest;
Chain 2 -> 1073
UniProt: Carbamoyl-phosphate synthase large chain;
Conserved-Region 133 -> 328
UniProt: ATP-grasp 1;
Nucleotide-Phosphate-Binding-Region 159 -> 216
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 285
UniProt: Manganese 1.
Metal-Binding-Site 299
UniProt: Manganese 1.
Metal-Binding-Site 301
UniProt: Manganese 2.
Protein-Segment 404 -> 553
UniProt: Oligomerization domain; Sequence Annotation Type: region of interest;
Protein-Segment 554 -> 936
UniProt: Carbamoyl phosphate synthetic domain; Sequence Annotation Type: region of interest;
Conserved-Region 679 -> 870
UniProt: ATP-grasp 2;
Nucleotide-Phosphate-Binding-Region 705 -> 762
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 829
UniProt: Manganese 3.
Metal-Binding-Site 841
UniProt: Manganese 3.
Metal-Binding-Site 843
UniProt: Manganese 4; Non-Experimental Qualifier: by similarity;
Protein-Segment 937 -> 1073
UniProt: Allosteric domain; Sequence Annotation Type: region of interest;
Acetylation-Modification 963

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0033 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10135; confirmed by SwissProt match.


Anderson75a: Anderson PM, Carlson JD (1975). "Reversible reaction of cyanate with a reactive sulfhydryl group at the glutamine binding site of carbamyl phosphate synthetase." Biochemistry 1975;14(16);3688-94. PMID: 240389

Anderson77: Anderson PM (1977). "Binding of allosteric effectors to carbamyl-phosphate synthetase from Escherichia coli." Biochemistry 1977;16(4);587-93. PMID: 189806

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Crabeel80: Crabeel M, Charlier D, Weyens G, Feller A, Pierard A, Glansdorff N (1980). "Use of gene cloning to determine polarity of an operon: genes carAB of Escherichia coli." J Bacteriol 1980;143(2);921-5. PMID: 6451616

Delannay99: Delannay S, Charlier D, Tricot C, Villeret V, Pierard A, Stalon V (1999). "Serine 948 and threonine 1042 are crucial residues for allosteric regulation of Escherichia coli carbamoylphosphate synthetase and illustrate coupling effects of activation and inhibition pathways." J Mol Biol 286(4);1217-28. PMID: 10047492

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eroglu02: Eroglu B, Powers-Lee SG (2002). "Unmasking a functional allosteric domain in an allosterically nonresponsive carbamoyl-phosphate synthetase." J Biol Chem 277(47);45466-72. PMID: 12244118

Fan09: Fan Y, Lund L, Shao Q, Gao YQ, Raushel FM (2009). "A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase." J Am Chem Soc 131(29);10211-9. PMID: 19569682

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Fresquet00: Fresquet V, Mora P, Rochera L, Ramon-Maiques S, Rubio V, Cervera J (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(4);979-91. PMID: 10843852

Garavaglia12: Garavaglia M, Rossi E, Landini P (2012). "The pyrimidine nucleotide biosynthetic pathway modulates production of biofilm determinants in Escherichia coli." PLoS One 7(2);e31252. PMID: 22359582

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gigot80: Gigot D, Crabeel M, Feller A, Charlier D, Lissens W, Glansdorff N, Pierard A (1980). "Patterns of polarity in the Escherichia coli car AB gene cluster." J Bacteriol 1980;143(2);914-20. PMID: 6162837

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guillou89: Guillou F, Rubino SD, Markovitz RS, Kinney DM, Lusty CJ (1989). "Escherichia coli carbamoyl-phosphate synthetase: domains of glutaminase and synthetase subunit interaction." Proc Natl Acad Sci U S A 86(21);8304-8. PMID: 2682645

Guillou92: Guillou F, Liao M, Garcia-Espana A, Lusty CJ (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 1992;31(6);1656-64. PMID: 1737023

Hart08: Hart EJ, Powers-Lee SG (2008). "Mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad?." Protein Sci 17(7);1120-8. PMID: 18458150

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Johnson07: Johnson JL, West JK, Nelson AD, Reinhart GD (2007). "Resolving the fluorescence response of Escherichia coli carbamoyl phosphate synthetase: mapping intra- and intersubunit conformational changes." Biochemistry 46(2);387-97. PMID: 17209549

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Khedouri66: Khedouri E, Anderson PM, Meister A (1966). "Selective inactivation of the glutamine binding site of Escherichia coli carbamyl phosphate synthetase by 2-amino-4-oxo-5-chloropentanoic acid." Biochemistry 1966;5(11);3552-7. PMID: 5339592

Kim04a: Kim J, Raushel FM (2004). "Access to the carbamate tunnel of carbamoyl phosphate synthetase." Arch Biochem Biophys 425(1);33-41. PMID: 15081891

Kothe04: Kothe M, Powers-Lee SG (2004). "Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase." Protein Sci 13(2);466-75. PMID: 14718657

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lund10: Lund L, Fan Y, Shao Q, Gao YQ, Raushel FM (2010). "Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation." J Am Chem Soc 132(11);3870-8. PMID: 20187643

Mareya95: Mareya SM, Raushel FM (1995). "Mapping the structural domains of E. coli carbamoyl phosphate synthetase using limited proteolysis." Bioorg Med Chem 3(5);525-32. PMID: 7648201

Marsh13: Marsh JA, Hernandez H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA (2013). "Protein complexes are under evolutionary selection to assemble via ordered pathways." Cell 153(2);461-70. PMID: 23582331

Meister89: Meister A (1989). "Mechanism and regulation of the glutamine-dependent carbamyl phosphate synthetase of Escherichia coli." Adv Enzymol Relat Areas Mol Biol 62;315-74. PMID: 2658488

Nyunoya83: Nyunoya H, Lusty CJ (1983). "The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase." Proc Natl Acad Sci U S A 1983;80(15);4629-33. PMID: 6308632

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Raushel79: Raushel FM, Rawding CJ, Anderson PM, Villafranca JJ (1979). "Paramagnetic probes for carbamoyl-phosphate synthetase: metal ion binding studies and preparation of nitroxide spin-labeled derivatives." Biochemistry 1979;18(25);5562-6. PMID: 229896

Rishavy00: Rishavy MA, Cleland WW, Lusty CJ (2000). "15N isotope effects in glutamine hydrolysis catalyzed by carbamyl phosphate synthetase: evidence for a tetrahedral intermediate in the mechanism." Biochemistry 39(24);7309-15. PMID: 10852731

Rochera02: Rochera L, Fresquet V, Rubio V, Cervera J (2002). "Mechanism of allosteric modulation of Escherichia coli carbamoyl phosphate synthetase probed by site-directed mutagenesis of ornithine site residues." FEBS Lett 514(2-3);323-8. PMID: 11943174

Rubino87: Rubino SD, Nyunoya H, Lusty CJ (1987). "In vivo synthesis of carbamyl phosphate from NH3 by the large subunit of Escherichia coli carbamyl phosphate synthetase." J Biol Chem 1987;262(9);4382-6. PMID: 3549732

SaeedKothe03: Saeed-Kothe A, Powers-Lee SG (2003). "Gain of glutaminase function in mutants of the ammonia-specific frog carbamoyl phosphate synthetase." J Biol Chem 278(29);26722-6. PMID: 12738780

Sahay98: Sahay N, Guy HI, Liu X, Evans DR (1998). "Regulation of an Escherichia coli/mammalian chimeric carbamoyl-phosphate synthetase." J Biol Chem 273(47);31195-202. PMID: 9813025

Shimada07: Shimada T, Hirao K, Kori A, Yamamoto K, Ishihama A (2007). "RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines." Mol Microbiol 66(3);744-57. PMID: 17919280

Thoden02: Thoden JB, Huang X, Raushel FM, Holden HM (2002). "Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia." J Biol Chem 277(42);39722-7. PMID: 12130656

Thoden04a: Thoden JB, Huang X, Kim J, Raushel FM, Holden HM (2004). "Long-range allosteric transitions in carbamoyl phosphate synthetase." Protein Sci 13(9);2398-405. PMID: 15322282

Thoden98: Thoden JB, Miran SG, Phillips JC, Howard AJ, Raushel FM, Holden HM (1998). "Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis." Biochemistry 37(25);8825-31. PMID: 9636022

Thoden99: Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM (1999). "The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution." Acta Crystallogr D Biol Crystallogr 1999;55 ( Pt 1);8-24. PMID: 10089390

Thoden99a: Thoden JB, Wesenberg G, Raushel FM, Holden HM (1999). "Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding." Biochemistry 38(8);2347-57. PMID: 10029528

Thoden99b: Thoden JB, Raushel FM, Wesenberg G, Holden HM (1999). "The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase." J Biol Chem 274(32);22502-7. PMID: 10428826

Trotta74: Trotta PP, Pinkus LM, Haschemeyer RH, Meister A (1974). "Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits." J Biol Chem 1974;249(2);492-9. PMID: 4358555

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Yefimenko05: Yefimenko I, Fresquet V, Marco-Marin C, Rubio V, Cervera J (2005). "Understanding carbamoyl phosphate synthetase deficiency: impact of clinical mutations on enzyme functionality." J Mol Biol 349(1);127-41. PMID: 15876373

Yu08a: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Other References Related to Gene Regulation

Bouvier84a: Bouvier J, Patte JC, Stragier P (1984). "Multiple regulatory signals in the control region of the Escherichia coli carAB operon." Proc Natl Acad Sci U S A 1984;81(13);4139-43. PMID: 6377309

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

Charlier88: Charlier D, Weyens G, Roovers M, Piette J, Bocquet C, Pierard A, Glansdorff N (1988). "Molecular interactions in the control region of the carAB operon encoding Escherichia coli carbamoylphosphate synthetase." J Mol Biol 1988;204(4);867-77. PMID: 3065519

Charlier92: Charlier D, Roovers M, Van Vliet F, Boyen A, Cunin R, Nakamura Y, Glansdorff N, Pierard A (1992). "Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression." J Mol Biol 1992;226(2);367-86. PMID: 1640456

Charlier93: Charlier D, Roovers M, Gigot D, Huysveld N, Pierard A, Glansdorff N (1993). "Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2." Mol Gen Genet 1993;237(1-2);273-86. PMID: 8455562

Charlier94: Charlier D, Huysveld N, Roovers M, Glansdorff N (1994). "On the role of the Escherichia coli integration host factor (IHF) in repression at a distance of the pyrimidine specific promoter P1 of the carAB operon." Biochimie 76(10-11);1041-51. PMID: 7748925

Charlier95: Charlier D, Hassanzadeh G, Kholti A, Gigot D, Pierard A, Glansdorff N (1995). "carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColEI multimers." J Mol Biol 1995;250(4);392-406. PMID: 7616564

Charlier95a: Charlier D, Gigot D, Huysveld N, Roovers M, Pierard A, Glansdorff N (1995). "Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region." J Mol Biol 1995;250(4);383-91. PMID: 7616563

Cho11: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102

Devroede04: Devroede N, Thia-Toong TL, Gigot D, Maes D, Charlier D (2004). "Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled." J Mol Biol 336(1);25-42. PMID: 14741201

Devroede06: Devroede N, Huysveld N, Charlier D (2006). "Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase." J Bacteriol 188(9);3236-45. PMID: 16621816

Han14a: Han X, Turnbough CL (2014). "Transcription start site sequence and spacing between the -10 region and the start site affect reiterative transcription-mediated regulation of gene expression in Escherichia coli." J Bacteriol 196(16);2912-20. PMID: 24891446

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

Nguyen10: Nguyen Le Minh P, Bervoets I, Maes D, Charlier D (2010). "The protein-DNA contacts in RutR{middle dot}carAB operator complexes." Nucleic Acids Res. PMID: 20472642

Nguyen15: Nguyen Le Minh P, de Cima S, Bervoets I, Maes D, Rubio V, Charlier D (2015). "Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli." FEBS Open Bio 5;76-84. PMID: 25685666

Shimada08: Shimada T, Ishihama A, Busby SJ, Grainger DC (2008). "The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions." Nucleic Acids Res 36(12);3950-5. PMID: 18515344

Wang98b: Wang H, Glansdorff N, Charlier D (1998). "The arginine repressor of Escherichia coli K-12 makes direct contacts to minor and major groove determinants of the operators." J Mol Biol 277(4);805-24. PMID: 9545374

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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