GenomeNet

Database: UniProt
Entry: P39831
LinkDB: P39831
Original site: P39831 
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   13-APR-2016, entry version 121.
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};
GN   OrderedLocusNames=b1539, JW1532;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
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.,
RA   Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K.,
RA   Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N.,
RA   Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J.,
RA   Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.;
RT   "A 570-kb DNA sequence of the Escherichia coli K-12 genome
RT   corresponding to 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.,
RA   Mau B., 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
RT   MG1655 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;
RA   Henrich B., Becker S., Schroeder U., Plapp R.;
RT   "dcp gene of Escherichia coli: cloning, sequencing, transcript
RT   mapping, and 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
RT   in the 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
RP   ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND
RP   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.,
RA   Wemmer D.E.;
RT   "The Rut pathway for pyrimidine degradation: novel chemistry and
RT   toxicity problems.";
RL   J. Bacteriol. 192:4089-4102(2010).
CC   -!- FUNCTION: NADP-dependent dehydrogenase with broad substrate
CC       specificity acting on 3-hydroxy acids. Catalyzes the NADP-
CC       dependent oxidation of L-allo-threonine to L-2-amino-3-keto-
CC       butyrate, which is spontaneously decarboxylated into aminoacetone.
CC       Also acts on D-threonine, L-serine, D-serine, D-3-
CC       hydroxyisobutyrate, L-3-hydroxyisobutyrate, D-glycerate and L-
CC       glycerate (PubMed:12535615). Able to catalyze the reduction of the
CC       malonic semialdehyde to 3-hydroxypropionic acid. YdfG is
CC       apparently supplementing RutE, the presumed malonic semialdehyde
CC       reductase involved in pyrimidine degradation since both are able
CC       to detoxify malonic semialdehyde (PubMed:20400551).
CC       {ECO:0000269|PubMed:12535615, ECO:0000269|PubMed:20400551}.
CC   -!- CATALYTIC ACTIVITY: 3-hydroxypropanoate + NADP(+) = 3-
CC       oxopropanoate + NADPH. {ECO:0000269|PubMed:20400551}.
CC   -!- CATALYTIC ACTIVITY: L-allo-threonine + NADP(+) = aminoacetone +
CC       CO(2) + NADPH. {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
CC         Celsius) {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
CC         from pH 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
CC       pyrimidine nucleosides and bases as the sole source of nitrogen at
CC       room temperature indicating a probably accumulation of a toxic
CC       intermediate, the malonic semialdehyde.
CC       {ECO:0000269|PubMed:20400551}.
CC   -!- MISCELLANEOUS: L-threonine, D-allo-threonine, DL-threo-3-phenyl-
CC       serine, malonate, DL-malate, citrate, isocitrate, DL-lactate, DL-
CC       tartrate, gluconate, glycerol and glycolate are inert as
CC       substrates.
CC   -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases
CC       (SDR) family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=X57947; Type=Frameshift; Positions=58; Evidence={ECO:0000305};
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_LN832404.1.
DR   ProteinModelPortal; P39831; -.
DR   SMR; P39831; 1-248.
DR   BioGrid; 4261740; 16.
DR   DIP; DIP-11696N; -.
DR   IntAct; P39831; 9.
DR   STRING; 511145.b1539; -.
DR   EPD; P39831; -.
DR   PaxDb; P39831; -.
DR   PRIDE; P39831; -.
DR   EnsemblBacteria; AAC74612; AAC74612; b1539.
DR   EnsemblBacteria; BAA15241; BAA15241; BAA15241.
DR   GeneID; 946085; -.
DR   KEGG; ecj:JW1532; -.
DR   KEGG; eco:b1539; -.
DR   PATRIC; 32118378; VBIEscCol129921_1609.
DR   EchoBASE; EB2249; -.
DR   EcoGene; EG12345; ydfG.
DR   eggNOG; ENOG4105EMU; Bacteria.
DR   eggNOG; COG4221; LUCA.
DR   InParanoid; P39831; -.
DR   KO; K16066; -.
DR   OMA; DWENMID; -.
DR   OrthoDB; EOG6N3CR8; -.
DR   PhylomeDB; P39831; -.
DR   BioCyc; EcoCyc:EG12345-MONOMER; -.
DR   BioCyc; ECOL316407:JW1532-MONOMER; -.
DR   BioCyc; MetaCyc:EG12345-MONOMER; -.
DR   PRO; PR:P39831; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; 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:0006212; P:uracil catabolic process; IDA:UniProtKB.
DR   Gene3D; 3.40.50.720; -; 1.
DR   InterPro; IPR016040; NAD(P)-bd_dom.
DR   InterPro; IPR020904; Sc_DH/Rdtase_CS.
DR   InterPro; IPR002347; SDR_fam.
DR   PANTHER; PTHR24322; PTHR24322; 2.
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   Complete proteome; Direct protein sequencing; NADP; Oxidoreductase;
KW   Reference proteome.
FT   CHAIN         1    248       NADP-dependent 3-hydroxy acid
FT                                dehydrogenase YdfG.
FT                                /FTId=PRO_0000054825.
FT   NP_BIND       7     12       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   NP_BIND      32     33       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   NP_BIND      54     55       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   NP_BIND     177    185       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   ACT_SITE    147    147       Proton acceptor. {ECO:0000255|PROSITE-
FT                                ProRule:PRU10001}.
FT   BINDING      81     81       NADP; via carbonyl oxygen.
FT                                {ECO:0000250|UniProtKB:Q05016}.
FT   BINDING     134    134       Substrate. {ECO:0000250}.
FT   BINDING     147    147       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   BINDING     151    151       NADP. {ECO:0000250|UniProtKB:Q05016}.
FT   CONFLICT    182    182       G -> T (in Ref. 4; X57947).
FT                                {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
//
DBGET integrated database retrieval system