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Escherichia coli K-12 substr. MG1655 Enzyme: acetylglutamate kinase


Gene: argB Accession Numbers: EG10064 (EcoCyc), b3959, ECK3950

Synonyms: N-acetylglutamate kinase, N-acetylglutamokinase, NAG kinase, AGK, ATP:N-acetyl-L-glutamate 5-phosphotransferase

Regulation Summary Diagram: ?

Subunit composition of acetylglutamate kinase = [ArgB]2
         acetylglutamate kinase monomer = ArgB

Summary:
Acetylglutamate kinase (ArgB) catalyzes the second step in ornithine and arginine biosynthesis.

ArgB catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate to generate N-acetylglutamyl-phosphate, with a specific activity of 1.1 µmol/s/mg [Gil99].

Acetylglutamate kinase comprises a homodimer of ArgB monomers, each of which lacks its amino-terminal methionine [Gil99].

Acetylglutamate kinase has been crystallized on its own, as well as bound to N-acetyl-L-glutamate, an ATP analong, ADP and a transition state analog [RamonMaiques02, GilOrtiz02]. The catalytic mechanism proposed based on these structures has been evaluated via site-directed mutagenesis [GilOrtiz03].

Gene Citations: [Natter77, Sens77]

Locations: cytosol

Map Position: [4,154,039 -> 4,154,812] (89.53 centisomes)
Length: 774 bp / 257 aa

Molecular Weight of Polypeptide: 27.028 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012967 , CGSC:1020 , EchoBASE:EB0062 , EcoGene:EG10064 , EcoliWiki:b3959 , Entrez-gene:948464 , Mint:MINT-1309378 , ModBase:P0A6C8 , OU-Microarray:b3959 , PortEco:argB , PR:PRO_000022127 , Pride:P0A6C8 , Protein Model Portal:P0A6C8 , RefSeq:NP_418394 , RegulonDB:EG10064 , SMR:P0A6C8 , String:511145.b3959 , UniProt:P0A6C8

Relationship Links: InterPro:IN-FAMILY:IPR001048 , InterPro:IN-FAMILY:IPR004662 , PDB:Structure:1GS5 , PDB:Structure:1GSJ , PDB:Structure:1OH9 , PDB:Structure:1OHA , PDB:Structure:1OHB , PDB:Structure:2WXB , PDB:Structure:2X2W , Pfam:IN-FAMILY:PF00696

In Paralogous Gene Group: 461 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006526 - arginine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Takahara07]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003991 - acetylglutamate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Gil99]
GO:0042803 - protein homodimerization activity Inferred from experiment [Gil99]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids arginine

Essentiality data for argB knockouts: ?

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

Credits:
Curated 22-Sep-2006 by Shearer A , SRI International
Last-Curated ? 30-Mar-2011 by Fulcher C , SRI International


Enzymatic reaction of: acetylglutamate kinase

EC Number: 2.7.2.8

N-acetyl-L-glutamate + ATP <=> N-acetylglutamyl-phosphate + ADP

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of arginine and polyamine biosynthesis , arginine biosynthesis I (via L-ornithine) , ornithine biosynthesis

Cofactors or Prosthetic Groups: Mg2+ [Gil99]

Kinetic Parameters:

Substrate
Km (μM)
Citations
N-acetyl-L-glutamate
1300.0
[GilOrtiz10, BRENDA14]
N-acetyl-L-glutamate
200.0
[MarcoMarin03, BRENDA14]
ATP
1100.0
[GilOrtiz10, BRENDA14]
ATP
290.0, 300.0
[MarcoMarin03, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 8
[MarcoMarin03, UniProt11]
Alternate sequence: L → R; UniProt: Reduces activity 50-fold. Increases KM for N-acetyl-L-glutamate and ATP about 10-fold.
Amino-Acid-Site 8
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;
Mutagenesis-Variant 66
[MarcoMarin03, UniProt11]
Alternate sequence: V → K; UniProt: Increases KM for N-acetyl-L- glutamate over 1000-fold. Increases KM for ATP nearly 20-fold.
Amino-Acid-Sites-That-Bind 66
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 158
[MarcoMarin03, UniProt11]
Alternate sequence: V → Q; UniProt: Increases KM for N-acetyl-L- glutamate over 1000-fold. Increases KM for ATP over 20-fold.
Amino-Acid-Sites-That-Bind 158
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 162
[MarcoMarin03, UniProt11]
Alternate sequence: Q → E; UniProt: Reduces activity over 99%. No effect on KM for N-acetyl-L-glutamate and ATP.
Amino-Acid-Site 217
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3959 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10064.


References

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." http://www.brenda-enzymes.org.

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

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

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

Gil99: Gil F, Ramon-Maiques S, Marina A, Fita I, Rubio V (1999). "N-Acetyl-L-glutamate kinase from Escherichia coli: cloning of the gene, purification and crystallization of the recombinant enzyme and preliminary X-ray analysis of the free and ligand-bound forms." Acta Crystallogr D Biol Crystallogr 1999;55 ( Pt 7);1350-2. PMID: 10393305

GilOrtiz02: Gil-Ortiz F, Fita I, Ramon-Maiques S, Marina A, Rubio V (2002). "A crystallographic glimpse of a nucleotide triphosphate (AMPPNP) bound to a protein surface: external and internal AMPPNP molecules in crystalline N-acetyl-L-glutamate kinase." Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 2);1892-5. PMID: 12351849

GilOrtiz03: Gil-Ortiz F, Ramon-Maiques S, Fita I, Rubio V (2003). "The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic." J Mol Biol 331(1);231-44. PMID: 12875848

GilOrtiz10: Gil-Ortiz F, Ramon-Maiques S, Fernandez-Murga ML, Fita I, Rubio V (2010). "Two crystal structures of Escherichia coli N-acetyl-L-glutamate kinase demonstrate the cycling between open and closed conformations." J Mol Biol 399(3);476-90. PMID: 20403363

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

MarcoMarin03: Marco-Marin C, Ramon-Maiques S, Tavarez S, Rubio V (2003). "Site-directed mutagenesis of Escherichia coli acetylglutamate kinase and aspartokinase III probes the catalytic and substrate-binding mechanisms of these amino acid kinase family enzymes and allows three-dimensional modelling of aspartokinase." J Mol Biol 334(3);459-76. PMID: 14623187

Natter77: Natter W, Sens D, James E (1977). "Metabolism of arginine-specific messenger ribonucleic acid in Escherichia coli K-12." J Bacteriol 1977;131(1);214-23. PMID: 326762

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

RamonMaiques02: Ramon-Maiques S, Marina A, Gil-Ortiz F, Fita I, Rubio V (2002). "Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis." Structure (Camb) 10(3);329-42. PMID: 12005432

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sens77: Sens D, Natter W, James E (1977). "In vitro transcription of the Escherichia coli K-12 argA, argE, and argCBH operons." J Bacteriol 1977;130(2);642-55. PMID: 400784

Takahara07: Takahara K, Akashi K, Yokota A (2007). "Continuous spectrophotometric assays for three regulatory enzymes of the arginine biosynthetic pathway." Anal Biochem 368(2);138-47. PMID: 17651682

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

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

Other References Related to Gene Regulation

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

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

Cunin83: Cunin R, Eckhardt T, Piette J, Boyen A, Pierard A, Glansdorff N (1983). "Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12." Nucleic Acids Res 1983;11(15);5007-19. PMID: 6348703

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

Piette82: Piette J, Cunin R, Boyen A, Charlier D, Crabeel M, Van Vliet F, Glansdorff N, Squires C, Squires CL (1982). "The regulatory region of the divergent argECBH operon in Escherichia coli K-12." Nucleic Acids Res 10(24);8031-48. PMID: 6761650

Weerasinghe06: Weerasinghe JP, Dong T, Schertzberg MR, Kirchhof MG, Sun Y, Schellhorn HE (2006). "Stationary phase expression of the arginine biosynthetic operon argCBH in Escherichia coli." BMC Microbiol 6;14. PMID: 16504055


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 29, 2014, biocyc15.