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



Gene: ydiB Accession Numbers: EG11234 (EcoCyc), b1692, ECK1690

Regulation Summary Diagram: ?

Subunit composition of shikimate dehydrogenase / quinate dehydrogenase = [YdiB]2

Summary:
Shikimate dehydrogenase 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]. Although YdiB can use both NAD+ or NADP+ for catalysis, it has higher catalytic efficiency with NAD+ [Michel03]. Because the intracellular concentration of NAD+ is reported to be 40-fold higher than that of NADH+, it is suggested that the dehydrogenase direction is favored by YdiB in vivo [Johansson06]. YdiB has lower catalytic efficiency than AroE, but has a broader substrate specificity [Michel03].

Crystal structures of the enzyme are presented at 2.3 Å and 2.5 Å resolution. The structure is discussed with respect to the enzyme catalytic mechanism [Benach03, Michel03]. Site-directed mutagenesis of predicted active-site residues suggested that catalysis does not involve a general acid-base mechanism [Lindner05].

Locations: cytosol

Map Position: [1,771,813 -> 1,772,679] (38.19 centisomes)
Length: 867 bp / 288 aa

Molecular Weight of Polypeptide: 31.228 kD (from nucleotide sequence), 31.3 kD (experimental) [Lindner05 ]

Molecular Weight of Multimer: 64 kD (experimental) [Michel03]

Unification Links: ASAP:ABE-0005651 , DIP:DIP-47967N , EchoBASE:EB1216 , EcoGene:EG11234 , EcoliWiki:b1692 , Mint:MINT-1283305 , ModBase:P0A6D5 , OU-Microarray:b1692 , PortEco:ydiB , Pride:P0A6D5 , Protein Model Portal:P0A6D5 , RefSeq:NP_416207 , RegulonDB:EG11234 , SMR:P0A6D5 , String:511145.b1692 , UniProt:P0A6D5

Relationship Links: InterPro:IN-FAMILY:IPR006151 , InterPro:IN-FAMILY:IPR013708 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR022872 , InterPro:IN-FAMILY:IPR022893 , PDB:Structure:1NPD , PDB:Structure:1O9B , PDB:Structure:1VI2 , 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: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:0009423 - chorismate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0000166 - nucleotide binding Inferred from experiment Inferred by computational analysis [GOA01a, Michel03]
GO:0004764 - shikimate 3-dehydrogenase (NADP+) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Michel03, Lindner05]
GO:0030266 - quinate 3-dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Lindner05]
GO:0050661 - NADP binding Inferred from experiment [Michel03]
GO:0051287 - NAD binding Inferred from experiment [Michel03]
GO:0052734 - shikimate 3-dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Michel03]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0052733 - quinate 3-dehydrogenase (NADP+) activity Inferred by computational analysis [GOA01, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids chorismate

Essentiality data for ydiB 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:
Created 06-Dec-2006 by Keseler I , SRI International
Curated 06-Dec-2006 by Keseler I , SRI International
Last-Curated ? 24-Jun-2013 by Kubo A , SRI International


Enzymatic reaction of: shikimate dehydrogenase

EC Number: 1.1.1.282

shikimate + NAD(P)+ <=> 3-dehydroshikimate + NAD(P)H + 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 opposite direction.

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

Summary:
Kinetic parameters have been measured by different authors. The Km for NAD+ is 87 µM, and the Km for NADP+ is 100 µM. The enzyme has a lower Km for shikimate in the presence of NAD+ [Michel03]. The Km for NAD+ was also reported to be 12.2 µM [Lindner05].

The Kcat of YdiB is reported to be about 4000-fold lower [Michel03] or only 7-fold lower [Benach03] than that of AroE.

Kinetic Parameters:

Substrate
Km (μM)
Citations
shikimate
2.9
[Lindner05]


Enzymatic reaction of: quinate dehydrogenase

EC Number: 1.1.1.282

L-quinate + NAD(P)+ <=> 3-dehydroquinate + NAD(P)H + H+

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

Reversibility of this reaction is unspecified.

Note: The enzyme may catalyze this reaction in vitro, but this reaction is not considered to be physiologically relevant.

Summary:
Kinetic parameters have been measured by different authors. The Km for NAD+ is 116 µM, and the Km for NADP+ is 500 µM. The enzyme has a 10-fold lower Km for quinate in the presence of NAD+ [Michel03]. The Km for NAD+ was also reported to be 18.4 µM [Lindner05].

Quinate is produced as a by-product in a genetically modified shikimate producing E. coli strain [Draths99]. Wild-type E. coli is not known to synthesize quinate or to use it as a source of carbon [Knop01]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-quinate
9.1
[Lindner05]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 67
[Lindner05, UniProt11]
Alternate sequence: S → A; UniProt: Reduces activity towards quinate about 6-fold.
Mutagenesis-Variant 71
[Lindner05, UniProt11]
Alternate sequence: K → A; UniProt: Increases KM for quinate 3200-fold. Increases KM for shikimate 170-fold.
Active-Site 71
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 92
[Lindner05, UniProt11]
Alternate sequence: N → A; UniProt: Alters protein structure. Loss of activity.
Mutagenesis-Variant 106
[Lindner05, UniProt11]
Alternate sequence: T → A; UniProt: Increases KM for quinate 2000-fold. Increases KM for shikimate 70-fold.
Mutagenesis-Variant 107
[Lindner05, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity towards quinate. Increases KM for shikimate 20000-fold.
Amino-Acid-Sites-That-Bind 107
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: probable;
Nucleotide-Phosphate-Binding-Region 131 -> 135
[UniProt10a]
UniProt: NAD;
Nucleotide-Phosphate-Binding-Region 155 -> 158
[UniProt10a]
UniProt: NAD;
Amino-Acid-Sites-That-Bind 205
[UniProt10a]
UniProt: NAD; via amide nitrogen;
Amino-Acid-Sites-That-Bind 235
[UniProt10a]
UniProt: NAD;
Nucleotide-Phosphate-Binding-Region 255 -> 259
[UniProt10a]
UniProt: NAD;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1692 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11234; 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

Benach03: Benach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF (2003). "The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase." J Biol Chem 278(21);19176-82. PMID: 12624088

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

Draths99: Draths KM, Knop DR, Frost JW (1999). "Shikimic Acid and Quinic Acid: Replacing Isolation from Plant Sources with Recombinant Microbial Biocatalysis." Journal of the American Chemical Society 121(7) 1603-1604.

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."

Johansson06: Johansson L, Liden G (2006). "Transcriptome analysis of a shikimic acid producing strain of Escherichia coli W3110 grown under carbon- and phosphate-limited conditions." J Biotechnol 126(4);528-45. PMID: 16828913

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

Knop01: Knop DR, Draths KM, Chandran SS, Barker JL, von Daeniken R, Weber W, Frost JW (2001). "Hydroaromatic equilibration during biosynthesis of shikimic acid." J Am Chem Soc 123(42);10173-82. PMID: 11603966

Lindner05: Lindner HA, Nadeau G, Matte A, Michel G, Menard R, Cygler M (2005). "Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli." J Biol Chem 280(8);7162-9. PMID: 15596430

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

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.

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 Thu Dec 18, 2014, BIOCYC14A.