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Escherichia coli K-12 substr. MG1655 Enzyme: shikimate dehydrogenase



Gene: aroE Accession Numbers: EG10077 (EcoCyc), b3281, ECK3268

Regulation Summary Diagram: ?

Summary:
Shikimate dehydrogenase (AroE) is involved in the 4th step of the chorismate pathway, which leads to the biosynthesis of aromatic amino acids. This enzyme converts 3-dehydroshikimate to shikimate by catalyzing the NADPH linked reduction of 3-dehydro-shikimate. [Yaniv55]

E. coli expresses two shikimate dehydrogenase paralogs, AroE and YdiB. AroE is NADP+ specific while YdiB uses either NADP+ or NAD+ as a co-substrate [Michel03]. The enzyme transfers hydrogen stereospecifically from the A-side of NADPH [Dansette74]. Shikimate dehydrogenase is constitutively expressed and the level of expression has been measured in minimal media [Tribe76].

The structure of AroE with bound NADP was determined at 1.5 Å resolution. Although AroE and YdiB have low sequence similarity, they have high structure similarity with two α/β domains separated by a wide cleft [Michel03].

Citations: [Anton88]

Gene Citations: [Kaczanowska04, Kaczanowska05]

Locations: cytosol

Map Position: [3,428,042 <- 3,428,860] (73.89 centisomes)
Length: 819 bp / 272 aa

Molecular Weight of Polypeptide: 29.414 kD (from nucleotide sequence), 32.0 kD (experimental) [Chaudhuri85 ]

Unification Links: ASAP:ABE-0010763 , CGSC:1004 , DIP:DIP-9153N , EchoBASE:EB0075 , EcoGene:EG10077 , EcoliWiki:b3281 , Mint:MINT-1246863 , ModBase:P15770 , OU-Microarray:b3281 , PortEco:aroE , PR:PRO_000022146 , Protein Model Portal:P15770 , RefSeq:NP_417740 , RegulonDB:EG10077 , SMR:P15770 , String:511145.b3281 , UniProt:P15770

Relationship Links: InterPro:IN-FAMILY:IPR006151 , InterPro:IN-FAMILY:IPR011342 , InterPro:IN-FAMILY:IPR013708 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR022893 , PDB:Structure:1NYT , Pfam:IN-FAMILY:PF01488 , Pfam:IN-FAMILY:PF08501

In Paralogous Gene Group: 513 (2 members)

Gene-Reaction Schematic: ?

Instance reaction of [shikimate + NAD(P)+ ← 3-dehydroshikimate + NAD(P)H + H+] (1.1.1.282):
i1: shikimate + NADP+ ↔ 3-dehydroshikimate + NADPH + H+ (1.1.1.25)

GO Terms:

Biological Process: GO:0009423 - chorismate biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Chaudhuri85]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0019632 - shikimate metabolic process Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0000166 - nucleotide binding Inferred from experiment [Michel03]
GO:0004764 - shikimate 3-dehydrogenase (NADP+) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Chaudhuri85]
GO:0050661 - NADP binding Inferred from experiment Inferred by computational analysis [GOA01a, Michel03]
GO:0016491 - oxidoreductase 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 chorismate

Essentiality data for aroE 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 No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Credits:
Last-Curated ? 24-Jun-2013 by Kubo A , SRI International


Enzymatic reaction of: shikimate dehydrogenase

Synonyms: shikimate-5-dehydrogenase, dehydroshikimate reductase, shikimate:NADP+ oxidoreductase, NADPH-dehydroshikimate reductase

EC Number: 1.1.1.25

shikimate + NADP+ <=> 3-dehydroshikimate + NADPH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Chaudhuri85]

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

pH(opt): 8.5 [BRENDA14, Yaniv55]


Sequence Features

Feature Class Location Citations Comment
Active-Site 65
[UniProt10b]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 102
[UniProt10b]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 126 -> 130
[UniProt10]
UniProt: NAD;
Nucleotide-Phosphate-Binding-Region 149 -> 154
[UniProt10]
UniProt: NAD;
Amino-Acid-Sites-That-Bind 189
[UniProt10]
UniProt: NAD; via amide nitrogen;
Amino-Acid-Sites-That-Bind 213
[UniProt10]
UniProt: NAD; via carbonyl oxygen;
Nucleotide-Phosphate-Binding-Region 237 -> 241
[UniProt10]
UniProt: NAD;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3281 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10077; confirmed by SwissProt match.


References

Anton88: Anton IA, Coggins JR (1988). "Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase." Biochem J 1988;249(2);319-26. PMID: 3277621

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.

Chaudhuri85: Chaudhuri S, Coggins JR (1985). "The purification of shikimate dehydrogenase from Escherichia coli." Biochem J 1985;226(1);217-23. PMID: 3883995

Dansette74: Dansette P, Azerad R (1974). "The shikimate pathway : II. Stereospecificity of hydrogen transfer catalyzed by NADPH-dehydroshikimate reductase of E. coli." Biochimie 1974;56(5);751-5. PMID: 4155957

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, 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."

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

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

Kaczanowska04: Kaczanowska M, Ryden-Aulin M (2004). "Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation." J Bacteriol 186(10);3046-55. PMID: 15126466

Kaczanowska05: Kaczanowska M, Ryden-Aulin M (2005). "The YrdC protein--a putative ribosome maturation factor." Biochim Biophys Acta 1727(2);87-96. PMID: 15716138

Michel03: Michel G, Roszak AW, Sauve V, Maclean J, Matte A, Coggins JR, Cygler M, Lapthorn AJ (2003). "Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities." J Biol Chem 278(21);19463-72. PMID: 12637497

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

Tribe76: Tribe DE, Camakaris H, Pittard J (1976). "Constitutive and repressivle enzymes of the common pathway of aromatic biosynthesis in Escherichia coli K-12: regulation of enzyme synthesis at different growth rates." J Bacteriol 127(3);1085-97. PMID: 8426

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

Yaniv55: Yaniv H, Gilvarg C (1955). "Aromatic biosynthesis. XIV. 5-Dehydroshikimic reductase." J Biol Chem 213(2);787-95. PMID: 14367339


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 Sun Dec 21, 2014, BIOCYC13A.