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Escherichia coli K-12 substr. MG1655 Enzyme: shikimate kinase II



Gene: aroL Accession Numbers: EG10082 (EcoCyc), b0388, ECK0383

Regulation Summary Diagram: ?

Summary:
Shikimate kinase is involved in the fifth step of the chorismate pathway, which leads to the biosynthesis of aromatic amino acids. Shikimate kinase catalyzes the formation of shikimate 3-phosphate from shikimate and ATP. There are two shikimate kinase enzymes, I (AroK) and II (AroL). The isoenzymes are separable and presumably monofunctional [Millar86].

The amino acid sequences of shikimate kinase I and II shows 30% homology over the entire length of both proteins [Whipp95]. Shikimate kinase I is encoded by aroK and shikimate kinase II is encoded by aroL. The expression of aroK unlike that of aroL, which is controlled by the TyrR and TrpR repressors, appears to be constitutive [Ely79, Lawley94]. Expression of aroL is regulated by the tyrR gene product protein with tyrosine or tryptophan as a co-repressor [Millar86].

Shikimate kinase I has a much lower affinity (approximately 100-fold) for shikimate than shikimate kinase II. Shikimate II seems to be the dominant enzyme of the pathway with shikimate I playing a secondary role. The enzyme activity is dependent on the presence of a divalent cation as a cofactor. [DeFeyter86]

Presumably the strains lacking the two major DAHP synthase isoenzymes (AroF and AroG) cannot accumulate an internal pool of shikimate that is sufficient for shikimate kinase I alone to carry out the phosphorylation, but the reaction can be performed by shikimate kinase II. Studies on the affinity of the shikimate kinase isoenzymes for shikimate support this interpretation. [DeFeyter86a]

The level of shikimate kinase can be repressed and derepressed. Both tyrosine and tryptophan, but not phenylalanine are apparently involved in this control. Starvation for both of these amino acids results in derepression. In a fully repressed cell, shikimate kinase I is the predominant shikimate kinase activity. However, a mutation in tyrR or the partial starvation of an aromatic auxotroph for tyrosine and tryptophan appears to alter only the level of shikimate kinase II which now becomes the cell's major shikimate kinase activity [Ely79]. In contrast to shikimate kinase II, the activity of shikimate kinase I in the cell is independent of both the amount of extracellular aromatic amino acids and the level of tyrR gene products [LobnerOlesen92a].

Amino acids and biosynthetic intermediates were tested for inhibitory effects. Neither the aromatic amino acids, either singly or all together, nor a mixture of aromatic amino acids and vitamins at the concentrations used caused inhibition of either shikimate kinase I or shikimate kinase II activity. Similarly neither chorismic acid nor prephenic acid, two key biosynthetic intermediates in the aromatic pathway, had a significant effect on these shikimate kinase activities. [DeFeyter86]

Citations: [DeFeyter86b]

Gene Citations: [DeFeyter86b]

Locations: cytosol

Map Position: [405,629 -> 406,153] (8.74 centisomes)
Length: 525 bp / 174 aa

Molecular Weight of Polypeptide: 19.151 kD (from nucleotide sequence), 21.4 kD (experimental) [DeFeyter86 ]

Isozyme Sequence Similarity:
shikimate kinase I: YES

Unification Links: ASAP:ABE-0001353 , CGSC:999 , EchoBASE:EB0080 , EcoGene:EG10082 , EcoliWiki:b0388 , ModBase:P0A6E1 , OU-Microarray:b0388 , PortEco:aroL , PR:PRO_000022151 , Pride:P0A6E1 , Protein Model Portal:P0A6E1 , RefSeq:NP_414922 , RegulonDB:EG10082 , SMR:P0A6E1 , String:511145.b0388 , Swiss-Model:P0A6E1 , UniProt:P0A6E1

Relationship Links: InterPro:IN-FAMILY:IPR000623 , InterPro:IN-FAMILY:IPR023000 , InterPro:IN-FAMILY:IPR027417 , InterPro:IN-FAMILY:IPR027544 , Pfam:IN-FAMILY:PF01202 , Prints:IN-FAMILY:PR01100 , Prosite:IN-FAMILY:PS01128

In Paralogous Gene Group: 523 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009073 - aromatic amino acid family biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Oldiges04]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009423 - chorismate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, DeFeyter86]
GO:0004765 - shikimate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, DeFeyter86]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, DeFeyter86]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids chorismate

Essentiality data for aroL 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 ? 24-Jun-2013 by Kubo A , SRI International


Enzymatic reaction of: shikimate kinase

EC Number: 2.7.1.71

shikimate + ATP <=> shikimate 3-phosphate + ADP + H+

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 chorismate metabolism , superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis , chorismate biosynthesis I , chorismate biosynthesis from 3-dehydroquinate

Citations: [Ely79, DeFeyter86a, DeFeyter86b, Millar86]

Cofactors or Prosthetic Groups: Mg2+ [DeFeyter86]

Cofactor Binding Comment: The enzyme activity was dependent on the presence of a divalent cation as a cofactor. Mg2+ was the most effective cation, but significant activity was obtained with all of the other divalent cations tested (Mn2+, Co2+, Fe2+, Ca2+, K+)

Kinetic Parameters:

Substrate
Km (μM)
Citations
shikimate
20000.0
[Pereira07, BRENDA14]
shikimate
5000.0, 200.0
[De87, BRENDA14]
shikimate
200.0
[DeFeyter86, BRENDA14]
ATP
160.0
[De87, BRENDA14]
ATP
160.0
[DeFeyter86, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[DeFeyter86, Millar86, UniProt11, Millar86]
UniProt: Removed.
Chain 2 -> 174
[UniProt09]
UniProt: Shikimate kinase 2;
Nucleotide-Phosphate-Binding-Region 12 -> 17
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 16
[UniProt10a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 32
[UniProt10a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 34
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 58
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 79
[UniProt10a]
UniProt: Substrate; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Protein-Segment 112 -> 126
[UniProt10a]
UniProt: LID domain; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 120
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 139
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0388 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10082; confirmed by SwissProt match.


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.

De87: De Feyter R (1987). "Shikimate kinases from Escherichia coli K12." Methods Enzymol 142;355-61. PMID: 3037263

DeFeyter86: DeFeyter RC, Pittard J (1986). "Purification and properties of shikimate kinase II from Escherichia coli K-12." J Bacteriol 1986;165(1);331-3. PMID: 3001029

DeFeyter86a: DeFeyter RC, Pittard J (1986). "Genetic and molecular analysis of aroL, the gene for shikimate kinase II in Escherichia coli K-12." J Bacteriol 1986;165(1);226-32. PMID: 3001024

DeFeyter86b: DeFeyter RC, Davidson BE, Pittard J (1986). "Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12." J Bacteriol 1986;165(1);233-9. PMID: 3001025

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

Ely79: Ely B, Pittard J (1979). "Aromatic amino acid biosynthesis: regulation of shikimate kinase in Escherichia coli K-12." J Bacteriol 1979;138(3);933-43. PMID: 222728

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, 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."

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

Lawley94: Lawley B, Pittard AJ (1994). "Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12." J Bacteriol 176(22);6921-30. PMID: 7961453

LobnerOlesen92a: Lobner-Olesen A, Marinus MG (1992). "Identification of the gene (aroK) encoding shikimic acid kinase I of Escherichia coli." J Bacteriol 1992;174(2);525-9. PMID: 1309529

Millar86: Millar G, Lewendon A, Hunter MG, Coggins JR (1986). "The cloning and expression of the aroL gene from Escherichia coli K12. Purification and complete amino acid sequence of shikimate kinase II, the aroL-gene product." Biochem J 1986;237(2);427-37. PMID: 3026317

Oldiges04: Oldiges M, Kunze M, Degenring D, Sprenger GA, Takors R (2004). "Stimulation, monitoring, and analysis of pathway dynamics by metabolic profiling in the aromatic amino acid pathway." Biotechnol Prog 20(6);1623-33. PMID: 15575692

Pereira07: Pereira JH, Vasconcelos IB, Oliveira JS, Caceres RA, de Azevedo WF, Basso LA, Santos DS (2007). "Shikimate kinase: a potential target for development of novel antitubercular agents." Curr Drug Targets 8(3);459-68. PMID: 17348838

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

UniProt10a: 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.

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

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."

Whipp95: Whipp MJ, Pittard AJ (1995). "A reassessment of the relationship between aroK- and aroL-encoded shikimate kinase enzymes of Escherichia coli." J Bacteriol 177(6);1627-9. PMID: 7883721

Other References Related to Gene Regulation

Chung13: Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S (2013). "dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLoS Comput Biol 9(10);e1003246. PMID: 24146601

Heatwole92: Heatwole VM, Somerville RL (1992). "Synergism between the Trp repressor and Tyr repressor in repression of the aroL promoter of Escherichia coli K-12." J Bacteriol 1992;174(1);331-5. PMID: 1530846

Jeeves99: Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI (1999). "Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences." Eur J Biochem 1999;265(3);919-28. PMID: 10518785

Yang96: Yang J, Gunasekera A, Lavoie TA, Jin L, Lewis DE, Carey J (1996). "In vivo and in vitro studies of TrpR-DNA interactions." J Mol Biol 258(1);37-52. PMID: 8613990


Report Errors or Provide Feedback
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 Fri Nov 28, 2014, biocyc11.