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Escherichia coli K-12 substr. MG1655 Enzyme: aspartate kinase III



Gene: lysC Accession Numbers: EG10550 (EcoCyc), b4024, ECK4016

Synonyms: apk, aspartokinase III

Regulation Summary Diagram: ?

Subunit composition of aspartate kinase III = [LysC]2

Summary:
Aspartokinase III (LysC) is one of three aspartokinase activities catalyzing the first step in the biosynthesis of lysine and homoserine, and indirectly methionine and threonine.

Aspartokinase III catalyzes the ATP-dependent phosphorylation of L-aspartate to yield L-aspartyl-4-phosphate [Richaud80, Theze74a, Stadtman61, Cassan86].

Aspartokinase III consists of a dimer of LysC monomers. In the presence of lysine, it can instead adopt an inactive tetrameric conformation [Richaud73, Niles73]. Structures have been determined for both this inactive tetrameric form of LysC and for the active dimer bound to aspartate and ADP, to 2.8 Å and 2.5 Å resolution, respectively. Each individual LysC monomer has an amino-terminal catalytic domain (residues 3-291) and a carboxy-terminal regulatory domain (residues 300-349) [Kotaka06]. The entire region of residues 318-352 is involved in feedback regulation by lysine, as is Glu-250 [Kikuchi99, OgawaMiyata01]. In the catalytic domain, Lys-8 and Asp-202 are important for enzyme function [MarcoMarin03].

A number of cis-dominant aspartokinase III mutants have been discovered [Cassan75, Boy79].

lysC gene expression is repressed by lysine, partially relieved from that repression by arginine, and derepressed substantially by combined methionine and threonine [Richaud80]. Despite this regulation, the lysC promoter has no apparent attenuator sequence [Cassan83].

Locations: cytosol

Map Position: [4,229,907 <- 4,231,256] (91.17 centisomes)
Length: 1350 bp / 449 aa

Molecular Weight of Polypeptide: 48.532 kD (from nucleotide sequence), 50 kD (experimental) [Richaud73 ]

Molecular Weight of Multimer: 105 kD (experimental) [Richaud73]

Isozyme Sequence Similarity:
ThrA: YES ,
MetL: YES

Unification Links: ASAP:ABE-0013156 , CGSC:539 , EchoBASE:EB0545 , EcoGene:EG10550 , EcoliWiki:b4024 , ModBase:P08660 , OU-Microarray:b4024 , PortEco:lysC , PR:PRO_000023138 , Pride:P08660 , Protein Model Portal:P08660 , RefSeq:NP_418448 , RegulonDB:EG10550 , SMR:P08660 , String:511145.b4024 , UniProt:P08660

Relationship Links: InterPro:IN-FAMILY:IPR001048 , InterPro:IN-FAMILY:IPR001341 , InterPro:IN-FAMILY:IPR002912 , InterPro:IN-FAMILY:IPR005260 , InterPro:IN-FAMILY:IPR018042 , PDB:Structure:2J0W , PDB:Structure:2J0X , Pfam:IN-FAMILY:PF00696 , Pfam:IN-FAMILY:PF01842 , Prosite:IN-FAMILY:PS00324 , Prosite:IN-FAMILY:PS51671

In Paralogous Gene Group: 564 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009089 - lysine biosynthetic process via diaminopimelate Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01, Richaud80]
GO:0009090 - homoserine biosynthetic process Inferred from experiment [Richaud80]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0009085 - lysine biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004072 - aspartate kinase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Richaud80]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016597 - amino acid binding Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids homoserine
metabolism biosynthesis of building blocks amino acids lysine

Essentiality data for lysC 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 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 10-Jul-2007 by Shearer A , SRI International


Enzymatic reaction of: aspartate kinase

Synonyms: aspartokinase

EC Number: 2.7.2.4

L-aspartate + ATP <=> L-aspartyl-4-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 S-adenosyl-L-methionine biosynthesis , threonine biosynthesis , superpathway of lysine, threonine and methionine biosynthesis I , aspartate superpathway , homoserine biosynthesis , lysine biosynthesis I

Summary:
The Ki for L-lysine is 0.391 mM [Chassagnole01].

Inhibitors (Allosteric): L-lysine [Kotaka06, Chassagnole01]

Inhibitors (Unknown Mechanism): L-leucine [Huang93] , S-(2-aminoethyl)-L-cysteine [Huang93]

Primary Physiological Regulators of Enzyme Activity: L-lysine

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-aspartyl-4-phosphate
17.0
[Chassagnole01]
ADP
250.0
[Angeles90]
L-aspartate
600.0
[Keng96, BRENDA14]
L-aspartate
320.0
[Chassagnole01]
L-aspartate
510.0, 630.0
0.16, 0.39
[James02, BRENDA14]
ATP
220.0
[Chassagnole01]

pH(opt): 7 [BRENDA14, Keng96]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10a]
UniProt: Removed;
Protein-Segment 2 -> 245
[UniProt10a]
UniProt: Aspartokinase; Sequence Annotation Type: region of interest;
Chain 2 -> 449
[UniProt10a]
UniProt: Lysine-sensitive aspartokinase 3;
Mutagenesis-Variant 8
[MarcoMarin03, UniProt11]
Alternate sequence: K → R; UniProt: Reduces activity about 98%. Increases KM for aspartate about 40-fold, enzyme is less sensitive to lysine inhibition.
Nucleotide-Phosphate-Binding-Region 8 -> 11
[UniProt10a]
UniProt: ATP;
Sequence-Conflict 14 -> 15
[Cassan83, UniProt10a]
Alternate sequence: VA → AS; UniProt: (in Ref. 5; CAA24910);
Sequence-Conflict 20
[Cassan83, UniProt10a]
Alternate sequence: M → E; UniProt: (in Ref. 5; CAA24910);
Amino-Acid-Sites-That-Bind 45
[UniProt10a]
UniProt: Substrate;
Sequence-Conflict 58
[Cassan86, UniProt10a]
Alternate sequence: G → C; UniProt: (in Ref. 1; AAA24095);
Mutagenesis-Variant 119
[MarcoMarin03, UniProt11]
Alternate sequence: E → D; UniProt: Increases KM for aspartate about 3000-fold.
Amino-Acid-Sites-That-Bind 119
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 198
[MarcoMarin03, UniProt11]
Alternate sequence: R → K; UniProt: Increases KM for aspartate about 200-fold.
Protein-Segment 198 -> 201
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 202
[MarcoMarin03, UniProt11]
Alternate sequence: D → E; UniProt: Reduces activity about 98%. Increases KM for aspartate about 40-fold, enzyme is less sensitive to lysine inhibition.
Nucleotide-Phosphate-Binding-Region 221 -> 222
[UniProt10a]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 227
[UniProt10a]
UniProt: ATP; via amide nitrogen and carbonyl oxygen;
Amino-Acid-Sites-That-Bind 232
[UniProt10a]
UniProt: ATP;
Protein-Segment 246 -> 449
[UniProt10]
UniProt: Interface; Sequence Annotation Type: region of interest;
Nucleotide-Phosphate-Binding-Region 257 -> 258
[UniProt10a]
UniProt: ATP;
Protein-Segment 299 -> 449
[UniProt10a]
UniProt: Required for homodimerization; Sequence Annotation Type: region of interest;
Conserved-Region 313 -> 394
[UniProt13]
UniProt: ACT.
Protein-Segment 318 -> 321
[UniProt10a]
UniProt: Allosteric inhibitor binding 1; Sequence Annotation Type: region of interest;
Protein-Segment 324 -> 325
[UniProt10a]
UniProt: Allosteric inhibitor binding 1; Sequence Annotation Type: region of interest;
Protein-Segment 338 -> 340
[UniProt10a]
UniProt: Allosteric inhibitor binding 2; Sequence Annotation Type: region of interest;
Protein-Segment 345 -> 346
[UniProt10a]
UniProt: Allosteric inhibitor binding 1; Sequence Annotation Type: region of interest;
Sequence-Conflict 401
[Cassan86, UniProt10a]
Alternate sequence: G → A; UniProt: (in Ref. 1; AAA24095);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4024 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10550; confirmed by SwissProt match.


References

Angeles90: Angeles TS, Viola RE (1990). "The kinetic mechanisms of the bifunctional enzyme aspartokinase-homoserine dehydrogenase I from Escherichia coli." Arch Biochem Biophys 283(1);96-101. PMID: 2241177

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

Boy79: Boy E, Borne F, Patte JC (1979). "Isolation and identification of mutants constitutive for aspartokinase III synthesis in Escherichia coli K 12." Biochimie 61(10);1151-60. PMID: 231461

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Cassan75: Cassan M, Boy E, Borne F, Patte JC (1975). "Regulation of the lysine biosynthetic pathway in Escherichia coli K-12: isolation of a cis-dominant constitutive mutant for AK III synthesis." J Bacteriol 123(2);391-9. PMID: 238953

Cassan83: Cassan M, Ronceray J, Patte JC (1983). "Nucleotide sequence of the promoter region of the E. coli lysC gene." Nucleic Acids Res 11(18);6157-66. PMID: 6312411

Cassan86: Cassan M, Parsot C, Cohen GN, Patte JC (1986). "Nucleotide sequence of lysC gene encoding the lysine-sensitive aspartokinase III of Escherichia coli K12. Evolutionary pathway leading to three isofunctional enzymes." J Biol Chem 1986;261(3);1052-7. PMID: 3003049

Chassagnole01: Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP (2001). "An integrated study of threonine-pathway enzyme kinetics in Escherichia coli." Biochem J 356(Pt 2);415-23. PMID: 11368768

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

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.

Huang93: Huang KJ, Hseu TH (1993). "Effects of lysine-sensitive aspartokinase III on lysine biosynthesis in Escherichia coli K-12." Proc Natl Sci Counc Repub China B 17(3);91-7. PMID: 8290655

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

James02: James CL, Viola RE (2002). "Production and characterization of bifunctional enzymes. Domain swapping to produce new bifunctional enzymes in the aspartate pathway." Biochemistry 41(11);3720-5. PMID: 11888289

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

Keng96: Keng YF, Viola RE (1996). "Specificity of aspartokinase III from Escherichia coli and an examination of important catalytic residues." Arch Biochem Biophys 335(1);73-81. PMID: 8914836

Kikuchi99: Kikuchi Y, Kojima H, Tanaka T (1999). "Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli." FEMS Microbiol Lett 173(1);211-5. PMID: 10220897

Kotaka06: Kotaka M, Ren J, Lockyer M, Hawkins AR, Stammers DK (2006). "Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine." J Biol Chem 281(42);31544-52. PMID: 16905770

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

Niles73: Niles EG, Westhead EW (1973). "The variable subunit structure of lysine-sensitive aspartylkinase from Escherichia coli TIR-8." Biochemistry 12(9);1715-22. PMID: 4572992

OgawaMiyata01: Ogawa-Miyata Y, Kojima H, Sano K (2001). "Mutation analysis of the feedback inhibition site of aspartokinase III of Escherichia coli K-12 and its use in L-threonine production." Biosci Biotechnol Biochem 65(5);1149-54. PMID: 11440130

Richaud73: Richaud C, Mazat JP, Gros C, Patte JC (1973). "Subunit structure of aspartokinase 3 of Escherichia coli K12." Eur J Biochem 40(2);619-29. PMID: 4360904

Richaud80: Richaud F, Phuc NH, Cassan M, Patte JC (1980). "Regulation of aspartokinase III synthesis in Escherichia coli: isolation of mutants containing lysC-lac fusions." J Bacteriol 143(1);513-5. PMID: 6249791

Stadtman61: Stadtman ER, Cohen GN, Lebras G (1961). "Feedback inhibition and repression of aspartokinase activity in Escherichia coli." Ann N Y Acad Sci 94;952-9. PMID: 13916055

Theze74a: Theze J, Margarita D, Cohen GN, Borne F, Patte JC (1974). "Mapping of the structural genes of the three aspartokinases and of the two homoserine dehydrogenases of Escherichia coli K-12." J Bacteriol 117(1);133-43. PMID: 4148765

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

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.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

Other References Related to Gene Regulation

Bouvier08: Bouvier J, Stragier P, Morales V, Remy E, Gutierrez C (2008). "Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator." J Bacteriol 190(15);5224-9. PMID: 18502871

Liao98: Liao HH, Hseu TH (1998). "Analysis of the regulatory region of the lysC gene of Escherichia coli." FEMS Microbiol Lett 1998;168(1);31-6. PMID: 9812360

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697


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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 Sat Dec 20, 2014, BIOCYC13A.