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Escherichia coli K-12 substr. MG1655 Enzyme: 3-hydroxy acid dehydrogenase

Gene: ydfG Accession Numbers: EG12345 (EcoCyc), b1539, ECK1532

Regulation Summary Diagram: ?

Subunit composition of 3-hydroxy acid dehydrogenase = [YdfG]4
         3-hydroxy acid dehydrogenase monomer = YdfG

The ydfG gene encodes a homotetrameric NADP+-dependent 3-hydroxy acid dehydrogenase. The high Km for NADP+ indicates that the enzyme acts in the reductive direction in vivo [Fujisawa03].

A ydfG deletion mutant only grows poorly with uridine as the sole source of nitrogen, likely due to toxicity of the pathway intermediate, malonic semialdehyde [Kim10e].

Locations: cytosol

Map Position: [1,625,541 -> 1,626,287] (35.04 centisomes)
Length: 747 bp / 248 aa

Molecular Weight of Polypeptide: 27.249 kD (from nucleotide sequence), 27 kD (experimental) [Fujisawa03 ]

Molecular Weight of Multimer: 105.0 kD (experimental) [Fujisawa03]

Unification Links: ASAP:ABE-0005137 , DIP:DIP-11696N , EchoBASE:EB2249 , EcoGene:EG12345 , EcoliWiki:b1539 , ModBase:P39831 , OU-Microarray:b1539 , PortEco:ydfG , Pride:P39831 , Protein Model Portal:P39831 , RefSeq:NP_416057 , RegulonDB:EG12345 , SMR:P39831 , String:511145.b1539 , Swiss-Model:P39831 , UniProt:P39831

Relationship Links: InterPro:IN-FAMILY:IPR002198 , InterPro:IN-FAMILY:IPR002347 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR020904 , Pfam:IN-FAMILY:PF00106 , Prints:IN-FAMILY:PR00080 , Prints:IN-FAMILY:PR00081 , Prosite:IN-FAMILY:PS00061

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006212 - uracil catabolic process Inferred from experiment [Kim10e]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0031132 - serine 3-dehydrogenase activity Inferred from experiment [Fujisawa03]
GO:0035527 - 3-hydroxypropionate dehydrogenase (NADP+) activity Inferred from experiment Inferred by computational analysis [GOA01a, Fujisawa03]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism metabolism of other compounds nitrogen metabolism

Essentiality data for ydfG 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]

Last-Curated ? 29-Apr-2010 by Keseler I , SRI International

Enzymatic reaction of: malonic semialdehyde reductase (3-hydroxy acid dehydrogenase)

EC Number:

3-hydroxypropanoate + NADP+ <=> malonate semialdehyde + NADPH + 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: uracil degradation III

Enzymatic reaction of: 3-hydroxy acid dehydrogenase

Synonyms: serine 3-dehydrogenase, L-serine:NADP+ 3-oxidoreductase

EC Number:

L-serine + NADP+ <=> 2-aminomalonate-semialdehyde + NADPH + 2 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.

Alternative Substrates for L-serine: (S)-3-hydroxybutanoate [Fujisawa03 ] , 3-hydroxy-isobutyrate [Fujisawa03 ] , D-threonine [Fujisawa03 ] , L-allo-threonine [Fujisawa03 ] , D-serine [Fujisawa03 ]

D-threonine and L-allo-threonine are the best substrates. The high Km for NADP+ indicates that the enzyme acts in the reductive direction in vivo [Fujisawa03].

Kinetic Parameters:

Km (μM)

pH(opt): 8.5 [Fujisawa03]

Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 4 -> 28
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 134
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Active-Site 147
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 182
[Henrich93, UniProt10a]
Alternate sequence: G → T; UniProt: (in Ref. 4);

Gene Local Context (not to scale): ?

Transcription Unit:


10/20/97 Gene b1539 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12345; confirmed by SwissProt match.


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

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

Fujisawa03: Fujisawa H, Nagata S, Misono H (2003). "Characterization of short-chain dehydrogenase/reductase homologues of Escherichia coli (YdfG) and Saccharomyces cerevisiae (YMR226C)." Biochim Biophys Acta 1645(1);89-94. PMID: 12535615

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, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Henrich93: Henrich B, Becker S, Schroeder U, Plapp R (1993). "dcp gene of Escherichia coli: cloning, sequencing, transcript mapping, and characterization of the gene product." J Bacteriol 175(22);7290-300. PMID: 8226676

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

Kim10e: Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE (2010). "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems." J Bacteriol 192(16):4089-102. PMID: 20400551

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.

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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 Mar 6, 2015, BIOCYC14A.