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Escherichia coli K-12 substr. MG1655 Enzyme: NAD-dependent dihydropyrimidine dehydrogenase


Subunit composition of NAD-dependent dihydropyrimidine dehydrogenase = [PreT]2[PreA]2
         NADH-dependent dihydropyrimidine dehydrogenase subunit = PreT (summary available)
         NADH-dependent dihydropyrimidine dehydrogenase subunit = PreA (summary available)

Summary:
The purified and reconstituted PreA/PreT complex was shown to have NAD-dependent dihydropyrimidine dehydrogenase activity [Mihara08, Hidese11]. The enzyme appears to produce dihydrouracil during exponential growth and during stationary phase convert it back to uracil, which can be incorporated into nucleic acids [Hidese11].

A preTA-deficient mutant has no growth defect in LB medium, but it is not producing dihydrouracil [Hidese11].

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Molecular Function:
Inferred from experimentGO:0004159 - dihydrouracil dehydrogenase (NAD+) activity [Hidese11, Mihara08]

Credits:
Created 19-Mar-2009 by Keseler I, SRI International
Last-Curated 05-Jan-2011 by Keseler I, SRI International


Enzymatic reaction of: dihydropyrimidine dehydrogenase

Inferred from experimentInferred by computational analysis

Synonyms: dihydrouracil dehydrogenase (NAD+), 5,6-dihydrouracil:NAD+ 5-oxidoreductase, DPD

EC Number: 1.3.1.1

5,6-dihydrouracil + NAD+ ⇄ uracil + NADH + H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Hidese11]

Alternative Substrates for uracil: 5-fluorouracil [Hidese11]

Summary:
NADP+ can not substitute for NAD+ [Mihara08].

Km for uracil was measured at pH 6.0, while the Km for 5.6-dihydrouracil was measured at pH 11.0 [Hidese11].

Kinetic Parameters:
Substrate Km (μM) Citations
uracil 38.0 [Hidese11]
5,6-dihydrouracil 160.0 [Hidese11]

Enzymatic reaction of: dihydropyrimidine dehydrogenase

Inferred from experiment

Synonyms: dihydrothymine dehydrogenase (NAD+)

EC Number: 1.3.1.1

5,6-dihydrothymine + NAD+ ⇄ thymine + NADH + H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Hidese11]

Summary:
Km for thymine was measured at pH 6.0, while the Km for 5.6-dihydrothymine was measured at pH 11.0 [Hidese11].

Kinetic Parameters:
Substrate Km (μM) Citations
5,6-dihydrothymine 130.0 [Hidese11]
thymine 87.0 [Hidese11]

Subunit of NAD-dependent dihydropyrimidine dehydrogenase: NADH-dependent dihydropyrimidine dehydrogenase subunit

Synonyms: PreT, YeiT

Gene: preT Accession Numbers: G7145 (EcoCyc), b2146, ECK2139

Locations: cytosol

Sequence Length: 412 AAs

Molecular Weight: 44.329 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred from experimentGO:0006208 - pyrimidine nucleobase catabolic process [Hidese11]
Inferred by computational analysisGO:0008152 - metabolic process [Reed03]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0003954 - NADH dehydrogenase activity [Hidese11]
Inferred from experimentGO:0005515 - protein binding [Lasserre06, Mihara08]
Inferred from experimentInferred by computational analysisGO:0051536 - iron-sulfur cluster binding [GOA01a, Mihara08]
Inferred by computational analysisGO:0004159 - dihydrouracil dehydrogenase (NAD+) activity [GOA01]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005737 - cytoplasm [Gaudet10]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Lasserre06]

MultiFun Terms: metabolism

Unification Links: DIP:DIP-28055N, EcoliWiki:b2146, ModBase:P76440, Protein Model Portal:P76440, RefSeq:NP_416651, SMR:P76440, UniProt:P76440

Relationship Links: InterPro:IN-FAMILY:IPR001327, InterPro:IN-FAMILY:IPR009051, InterPro:IN-FAMILY:IPR016040, InterPro:IN-FAMILY:IPR023753, InterPro:IN-FAMILY:IPR028261, Pfam:IN-FAMILY:PF07992, Pfam:IN-FAMILY:PF14691

Summary:
Based on sequence similarity, PreT was predicted to be a dihydrothymine dehydrogenase or glutamate synthase [Reed03, Serres01]. PreT has similarity to the N-terminal half of mammalian dihydropyrimidine dehydrogenase [Hidese11].

PreT was shown to be in a complex with PreA [Lasserre06, Mihara08].

Expression of preT is 20-fold higher in a biofilm than during exponential growth in liquid culture [Schembri03].

Essentiality data for preT knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of NAD-dependent dihydropyrimidine dehydrogenase: NADH-dependent dihydropyrimidine dehydrogenase subunit

Synonyms: PreA, YeiA

Gene: preA Accession Numbers: EG11289 (EcoCyc), b2147, ECK2140

Locations: cytosol

Sequence Length: 411 AAs

Molecular Weight: 45.069 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred from experimentGO:0006208 - pyrimidine nucleobase catabolic process [Hidese11]
Inferred from experimentGO:0006928 - movement of cell or subcellular component [Inoue07]
Inferred by computational analysisGO:0008152 - metabolic process [Serres01]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0003954 - NADH dehydrogenase activity [Hidese11]
Inferred from experimentGO:0005515 - protein binding [Lasserre06, Mihara08]
Inferred from experimentInferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, Mihara08]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0004159 - dihydrouracil dehydrogenase (NAD+) activity [GOA01, Reed03]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005737 - cytoplasm [GOA01a, Gaudet10]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolism

Unification Links: DIP:DIP-11915N, EcoliWiki:b2147, ModBase:P25889, Protein Model Portal:P25889, RefSeq:NP_416652, SMR:P25889, UniProt:P25889

Relationship Links: InterPro:IN-FAMILY:IPR005720, InterPro:IN-FAMILY:IPR013785, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, Pfam:IN-FAMILY:PF01180, Pfam:IN-FAMILY:PF14697, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

Summary:
Based on sequence similarity, PreA was predicted to be a dihydrothymine/dihydropyrimidine dehydrogenase [Reed03, Serres01]. PreA has similarity to the C-terminal half of mammalian dihydropyrimidine dehydrogenase [Hidese11].

PreA was shown to be in a complex with PreT [Lasserre06, Mihara08] and is required for swarming motility [Inoue07].

Essentiality data for preA knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

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

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Hidese11: Hidese R, Mihara H, Kurihara T, Esaki N (2011). "Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil." J Bacteriol 193(4);989-93. PMID: 21169495

Inoue07: Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K (2007). "Genome-wide screening of genes required for swarming motility in Escherichia coli K-12." J Bacteriol 189(3);950-7. PMID: 17122336

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Mihara08: Mihara H, Hidese R, Yamane M, Kurihara T, Esaki N (2008). "The iscS gene deficiency affects the expression of pyrimidine metabolism genes." Biochem Biophys Res Commun 372(3);407-11. PMID: 18482579

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

Schembri03: Schembri MA, Kjaergaard K, Klemm P (2003). "Global gene expression in Escherichia coli biofilms." Mol Microbiol 48(1);253-67. PMID: 12657059

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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