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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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MetaCyc Pathway: quinate degradation II

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Aromatic Compounds Degradation Quinate Degradation

Some taxa known to possess this pathway include ? : Amycolatopsis methanolica , Aspergillus nidulans , Corynebacterium glutamicum , Corynebacterium glutamicum R , Neurospora crassa

Expected Taxonomic Range: Actinobacteria , Firmicutes , Fungi

Summary:
General Background

L-quinate is a naturally occuring compound found in decaying plant matter [Hawkins93]. Quinate is one of several aromatic compounds that can be metabolized by microorganisms to the central intermediate protocatechuate that can be further metabolized via the β-ketoadipate pathway to acetyl-CoA and succinyl-CoA [Tresguerres70, Adachi03]. Bacteria capable of using quinate as a sole carbon source were observed as early as 1911 [Beijerinck11]

Quinate degradation was initially studied in the fungus Neurospora crassa [Tatum54], and later in other fungi (such as Aspergillus nidulans [Hawkins85]) and bacteria, including Acinetobacter sp. ADP1 (at the time reported as Acinetobacter calcoaceticus) [Elsemore95, Elsemore94], Gluconobacter oxydans [Adachi03] and Corynebacterium glutamicum [Schoepe08].| Many of these organisms can grow on quinate as a sole carbon and energy source, and the pathway is inducible by growth on either L-quinate, shikimate, or protocatechuate.

Two variants of this pathway are present in MetaCyc; the main difference between them lies in the enzyme that catalyzes the initial oxidation of L-quinate. Filamentous fungi and Gram-positive bacteria use an NAD(P)-dependent enzyme (EC 1.1.1.24), while Gram-negative bacteria use a pyrroloquinoline quinone (PQQ)-dependent enzyme (EC 1.1.99.25) [vanKleef88]. The later pathway is desribed in quinate degradation I.

About This Pathway

Quinate degradation was first studied in filamentous fungi such as Neurospora crassa and Aspergillus nidulans. The fungal pathway starts with conversion of L-quinate to 3-dehydroquinate by an NAD-dependent quinate/shikimate dehydrogenase (EC 1.1.1.24). The genes involved in the fungal pathway (qa genes in Neurospora crassa, qut genes in Aspergillus nidulans ) were shown to be present in a single cluster, and are induced by growth on either L-quinate or shikimate [Patel81, Wheeler96, Hawkins93]. The clusters include a gene encoding a permease that enables L-quinate to enter the organism [Whittington87].

An NAD-dependent enzyme is also present in certain Gram-positive bacteria, such as Corynebacterium glutamicum [Teramoto09]. As in the fungi, the qsuD gene, which encodes the Corynebacterium glutamicum enzyme, is located in a gene cluster that also contains the genes encoding the rest of the pathway's enzymes. The cluster, which is under the control of the QsuR regulator, is induced by growth on L-quinate shikimate [Teramoto09].

Variants: quinate degradation I

Credits:
Created 07-Jan-2010 by Caspi R , SRI International


References

Adachi03: Adachi O, Tanasupawat S, Yoshihara N, Toyama H, Matsushita K (2003). "3-dehydroquinate production by oxidative fermentation and further conversion of 3-dehydroquinate to the intermediates in the shikimate pathway." Biosci Biotechnol Biochem 67(10);2124-31. PMID: 14586099

Beijerinck11: Beijerinck, M. W. (1911). "Pigments to Products of Oxidation by Bacterial Action." Proc. Acad. Wetenschappen, 13:1066-1077.

Elsemore94: Elsemore DA, Ornston LN (1994). "The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate-shikimate dehydrogenase." J Bacteriol 1994;176(24);7659-66. PMID: 8002591

Elsemore95: Elsemore DA, Ornston LN (1995). "Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calcoaceticus." J Bacteriol 177(20);5971-8. PMID: 7592351

Hawkins85: Hawkins AR, Francisco Da Silva AJ, Roberts CF (1985). "Cloning and characterization of the three enzyme structural genes QUTB, QUTC and QUTE from the quinic acid utilization gene cluster in Aspergillus nidulans." Curr Genet 9(4);305-11. PMID: 3916726

Hawkins93: Hawkins AR, Lamb HK, Moore JD, Charles IG, Roberts CF (1993). "The pre-chorismate (shikimate) and quinate pathways in filamentous fungi: theoretical and practical aspects." J Gen Microbiol 139(12);2891-9. PMID: 8126417

Patel81: Patel VB, Schweizer M, Dykstra CC, Kushner SR, Giles NH (1981). "Genetic organization and transcriptional regulation in the qa gene cluster of Neurospora crassa." Proc Natl Acad Sci U S A 78(9);5783-7. PMID: 6458044

Schoepe08: Schoepe J, Niefind K, Schomburg D (2008). "1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum." Acta Crystallogr D Biol Crystallogr D64(Pt 7);803-9. PMID: 18566515

Tatum54: Tatum EL, Gross SR, Ehrensvard G, Garnjobst L (1954). "Synthesis of aromatic compounds by Neurospora." Proc Natl Acad Sci U S A 40(5);271-6. PMID: 16589471

Teramoto09: Teramoto H, Inui M, Yukawa H (2009). "Regulation of expression of genes involved in quinate and shikimate utilization in Corynebacterium glutamicum." Appl Environ Microbiol 75(11);3461-8. PMID: 19376919

Tresguerres70: Tresguerres, M.E.F., Torrontegui, G.D., Canovas, J.L. (1970). "The Metabolism of Quinate by Acinetobacter calco-aceticus." Arch. Mikrobiol. 70:110-118.

vanKleef88: van Kleef MA, Duine JA (1988). "Bacterial NAD(P)-independent quinate dehydrogenase is a quinoprotein." Arch Microbiol 150(1);32-6. PMID: 3044290

Wheeler96: Wheeler KA, Lamb HK, Hawkins AR (1996). "Control of metabolic flux through the quinate pathway in Aspergillus nidulans." Biochem J 315 ( Pt 1);195-205. PMID: 8670107

Whittington87: Whittington HA, Grant S, Roberts CF, Lamb H, Hawkins AR (1987). "Identification and isolation of a putative permease gene in the quinic acid utilization (QUT) gene cluster of Aspergillus nidulans." Curr Genet 12(2);135-9. PMID: 2835177

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Adachi08: Adachi O, Ano Y, Toyama H, Matsushita K (2008). "A novel 3-dehydroquinate dehydratase catalyzing extracellular formation of 3-dehydroshikimate by oxidative fermentation of Gluconobacter oxydans IFO 3244." Biosci Biotechnol Biochem 72(6);1475-82. PMID: 18540103

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

Chaudhuri86: Chaudhuri S, Lambert JM, McColl LA, Coggins JR (1986). "Purification and characterization of 3-dehydroquinase from Escherichia coli." Biochem J 1986;239(3);699-704. PMID: 2950851

Duncan86: Duncan K, Chaudhuri S, Campbell MS, Coggins JR (1986). "The overexpression and complete amino acid sequence of Escherichia coli 3-dehydroquinase." Biochem J 1986;238(2);475-83. PMID: 3541912

Editors93: Editors: Abraham L. Sonenshein, James A. Hoch, Richard Losick (1993). "Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics." American Society For Microbiology, Washington, DC 20005.

Euverink92: Euverink GJ, Hessels GI, Vrijbloed JW, Coggins JR, Dijkhuizen L (1992). "Purification and characterization of a dual function 3-dehydroquinate dehydratase from Amycolatopsis methanolica." J Gen Microbiol 138(11);2449-57. PMID: 1479361

Geever89: Geever RF, Huiet L, Baum JA, Tyler BM, Patel VB, Rutledge BJ, Case ME, Giles NH (1989). "DNA sequence, organization and regulation of the qa gene cluster of Neurospora crassa." J Mol Biol 207(1);15-34. PMID: 2525625

Hawkins88: Hawkins AR, Lamb HK, Smith M, Keyte JW, Roberts CF (1988). "Molecular organisation of the quinic acid utilization (QUT) gene cluster in Aspergillus nidulans." Mol Gen Genet 214(2);224-31. PMID: 2976880

Hawkins93a: Hawkins AR, Moore JD, Adeokun AM (1993). "Characterization of the 3-dehydroquinase domain of the pentafunctional AROM protein, and the quinate dehydrogenase from Aspergillus nidulans, and the overproduction of the type II 3-dehydroquinase from neurospora crassa." Biochem J 296 ( Pt 2);451-7. PMID: 8257437

Kinghorn81: Kinghorn JR, Schweizer M, Giles NH, Kushner SR (1981). "The cloning and analysis of the aroD gene of E. coli K-12." Gene 14(1-2);73-80. PMID: 7021325

Kleanthous92: Kleanthous C, Deka R, Davis K, Kelly SM, Cooper A, Harding SE, Price NC, Hawkins AR, Coggins JR (1992). "A comparison of the enzymological and biophysical properties of two distinct classes of dehydroquinase enzymes." Biochem J 282 ( Pt 3);687-95. PMID: 1554351

Larimer83: Larimer FW, Morse CC, Beck AK, Cole KW, Gaertner FH (1983). "Isolation of the ARO1 cluster gene of Saccharomyces cerevisiae." Mol Cell Biol 3(9);1609-14. PMID: 6355828

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lim02: Lim EK, Doucet CJ, Li Y, Elias L, Worrall D, Spencer SP, Ross J, Bowles DJ (2002). "The activity of Arabidopsis glycosyltransferases toward salicylic acid, 4-hydroxybenzoic acid, and other benzoates." J Biol Chem 277(1);586-92. PMID: 11641410

MITSUHASHI54: MITSUHASHI S, DAVIS BD (1954). "Aromatic biosynthesis. XII. Conversion of 5-dehydroquinic acid to 5-dehydroshikimic acid dy 5-dehydroquinase." Biochim Biophys Acta 15(1);54-61. PMID: 13198937

Pfleger08: Pfleger BF, Kim Y, Nusca TD, Maltseva N, Lee JY, Rath CM, Scaglione JB, Janes BK, Anderson EC, Bergman NH, Hanna PC, Joachimiak A, Sherman DH (2008). "Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis." Proc Natl Acad Sci U S A 105(44);17133-8. PMID: 18955706

Porat04: Porat I, Waters BW, Teng Q, Whitman WB (2004). "Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis." J Bacteriol 186(15);4940-50. PMID: 15262931

Rutledge84: Rutledge BJ (1984). "Molecular characterization of the qa-4 gene of Neurospora crassa." Gene 32(3);275-87. PMID: 6241580

Singh06: Singh SA, Christendat D (2006). "Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway." Biochemistry 45(25);7787-96. PMID: 16784230

Singh07: Singh, S.A., Christendat, D. (2007). "The DHQ-dehydroshikimate-SDH-shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway." Crystal Growth and Design. 7(11):2153-2160.

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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC13A.