YDFG_ECOLI
ID YDFG_ECOLI Reviewed; 248 AA.
AC P39831; P77149; P78161; P78162;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=NADP-dependent 3-hydroxy acid dehydrogenase YdfG {ECO:0000303|PubMed:12535615};
DE AltName: Full=L-allo-threonine dehydrogenase {ECO:0000303|PubMed:12535615};
DE EC=1.1.1.381 {ECO:0000269|PubMed:12535615};
DE AltName: Full=Malonic semialdehyde reductase {ECO:0000303|PubMed:20400551};
DE EC=1.1.1.298 {ECO:0000305|PubMed:20400551};
GN Name=ydfG {ECO:0000312|EMBL:AAC74612.1}; OrderedLocusNames=b1539, JW1532;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-182.
RC STRAIN=K12;
RX PubMed=8226676; DOI=10.1128/jb.175.22.7290-7300.1993;
RA Henrich B., Becker S., Schroeder U., Plapp R.;
RT "dcp gene of Escherichia coli: cloning, sequencing, transcript mapping, and
RT characterization of the gene product.";
RL J. Bacteriol. 175:7290-7300(1993).
RN [5]
RP IDENTIFICATION.
RX PubMed=7984428; DOI=10.1093/nar/22.22.4756;
RA Borodovsky M., Rudd K.E., Koonin E.V.;
RT "Intrinsic and extrinsic approaches for detecting genes in a bacterial
RT genome.";
RL Nucleic Acids Res. 22:4756-4767(1994).
RN [6]
RP PROTEIN SEQUENCE OF 1-12.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP PROTEIN SEQUENCE OF 1-14, FUNCTION AS A DEHYDROGENASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=12535615; DOI=10.1016/s1570-9639(02)00533-2;
RA Fujisawa H., Nagata S., Misono H.;
RT "Characterization of short-chain dehydrogenase/reductase homologues of
RT Escherichia coli (YdfG) and Saccharomyces cerevisiae (YMR226C).";
RL Biochim. Biophys. Acta 1645:89-94(2003).
RN [8]
RP FUNCTION IN PYRIMIDINE CATABOLISM, AND DISRUPTION PHENOTYPE.
RX PubMed=20400551; DOI=10.1128/jb.00201-10;
RA Kim K.S., Pelton J.G., Inwood W.B., Andersen U., Kustu S., Wemmer D.E.;
RT "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity
RT problems.";
RL J. Bacteriol. 192:4089-4102(2010).
CC -!- FUNCTION: NADP-dependent dehydrogenase with broad substrate specificity
CC acting on 3-hydroxy acids. Catalyzes the NADP-dependent oxidation of L-
CC allo-threonine to L-2-amino-3-keto-butyrate, which is spontaneously
CC decarboxylated into aminoacetone. Also acts on D-threonine, L-serine,
CC D-serine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D-glycerate
CC and L-glycerate (PubMed:12535615). Able to catalyze the reduction of
CC the malonic semialdehyde to 3-hydroxypropionic acid. YdfG is apparently
CC supplementing RutE, the presumed malonic semialdehyde reductase
CC involved in pyrimidine degradation since both are able to detoxify
CC malonic semialdehyde (PubMed:20400551). {ECO:0000269|PubMed:12535615,
CC ECO:0000269|PubMed:20400551}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-hydroxypropanoate + NADP(+) = 3-oxopropanoate + H(+) +
CC NADPH; Xref=Rhea:RHEA:26438, ChEBI:CHEBI:15378, ChEBI:CHEBI:16510,
CC ChEBI:CHEBI:33190, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC EC=1.1.1.298; Evidence={ECO:0000269|PubMed:20400551};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-allo-threonine + NADP(+) = aminoacetone + CO2 + NADPH;
CC Xref=Rhea:RHEA:43524, ChEBI:CHEBI:16526, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58320, ChEBI:CHEBI:58349, ChEBI:CHEBI:58585;
CC EC=1.1.1.381; Evidence={ECO:0000269|PubMed:12535615};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.54 mM for NADP(+) (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=40 mM for L-serine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=69 mM for D-serine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=60 mM for D-threonine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=29 mM for L-allo-threonine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=33 mM for L-glycerate (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=50 mM for D-glycerate (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=60 mM for L-3-hydroxyisobutyrate (at pH 9 and at 30 degrees
CC Celsius) {ECO:0000269|PubMed:12535615};
CC KM=61 mM for D-3-hydroxyisobutyrate (at pH 9 and at 30 degrees
CC Celsius) {ECO:0000269|PubMed:12535615};
CC Note=The highest catalytic efficiency was observed with L-allo-
CC threonine. {ECO:0000269|PubMed:12535615};
CC pH dependence:
CC Optimum pH is about 8.5 for the oxidation of L-serine. Stable from pH
CC 6.5 to 10.0. {ECO:0000269|PubMed:12535615};
CC Temperature dependence:
CC Still active after heating at 55 degrees Celsius for 80 minutes.
CC {ECO:0000269|PubMed:12535615};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12535615}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene grow poorly on pyrimidine
CC nucleosides and bases as the sole source of nitrogen at room
CC temperature indicating a probably accumulation of a toxic intermediate,
CC the malonic semialdehyde. {ECO:0000269|PubMed:20400551}.
CC -!- MISCELLANEOUS: L-threonine, D-allo-threonine, DL-threo-3-phenyl-serine,
CC malonate, DL-malate, citrate, isocitrate, DL-lactate, DL-tartrate,
CC gluconate, glycerol and glycolate are inert as substrates.
CC -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR)
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=X57947; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74612.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15241.1; -; Genomic_DNA.
DR EMBL; X57947; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; F64908; F64908.
DR RefSeq; NP_416057.1; NC_000913.3.
DR RefSeq; WP_000636571.1; NZ_STEB01000003.1.
DR AlphaFoldDB; P39831; -.
DR SMR; P39831; -.
DR BioGRID; 4261740; 23.
DR BioGRID; 850445; 1.
DR DIP; DIP-11696N; -.
DR IntAct; P39831; 13.
DR STRING; 511145.b1539; -.
DR jPOST; P39831; -.
DR PaxDb; P39831; -.
DR PRIDE; P39831; -.
DR EnsemblBacteria; AAC74612; AAC74612; b1539.
DR EnsemblBacteria; BAA15241; BAA15241; BAA15241.
DR GeneID; 66674600; -.
DR GeneID; 946085; -.
DR KEGG; ecj:JW1532; -.
DR KEGG; eco:b1539; -.
DR PATRIC; fig|1411691.4.peg.726; -.
DR EchoBASE; EB2249; -.
DR eggNOG; COG4221; Bacteria.
DR HOGENOM; CLU_010194_2_10_6; -.
DR InParanoid; P39831; -.
DR OMA; WRWMWET; -.
DR PhylomeDB; P39831; -.
DR BioCyc; EcoCyc:EG12345-MON; -.
DR BioCyc; MetaCyc:EG12345-MON; -.
DR BRENDA; 1.1.1.381; 2026.
DR PRO; PR:P39831; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0008442; F:3-hydroxyisobutyrate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0035527; F:3-hydroxypropionate dehydrogenase (NADP+) activity; IDA:EcoCyc.
DR GO; GO:0031132; F:serine 3-dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0030497; P:fatty acid elongation; IBA:GO_Central.
DR GO; GO:0006212; P:uracil catabolic process; IDA:UniProtKB.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR020904; Sc_DH/Rdtase_CS.
DR InterPro; IPR002347; SDR_fam.
DR Pfam; PF00106; adh_short; 1.
DR PRINTS; PR00081; GDHRDH.
DR PRINTS; PR00080; SDRFAMILY.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00061; ADH_SHORT; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..248
FT /note="NADP-dependent 3-hydroxy acid dehydrogenase YdfG"
FT /id="PRO_0000054825"
FT ACT_SITE 147
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10001"
FT BINDING 7..12
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 32..33
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 54..55
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 81
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 134
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 147
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 151
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT BINDING 177..185
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q05016"
FT CONFLICT 182
FT /note="G -> T (in Ref. 4; X57947)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 248 AA; 27249 MW; 6FECC5FBAA86EA42 CRC64;
MIVLVTGATA GFGECITRRF IQQGHKVIAT GRRQERLQEL KDELGDNLYI AQLDVRNRAA
IEEMLASLPA EWCNIDILVN NAGLALGMEP AHKASVEDWE TMIDTNNKGL VYMTRAVLPG
MVERNHGHII NIGSTAGSWP YAGGNVYGAT KAFVRQFSLN LRTDLHGTAV RVTDIEPGLV
GGTEFSNVRF KGDDGKAEKT YQNTVALTPE DVSEAVWWVS TLPAHVNINT LEMMPVTQSY
AGLNVHRQ
