YM71_YEAST
ID YM71_YEAST Reviewed; 267 AA.
AC Q05016; D6W051;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=NADP-dependent 3-hydroxy acid dehydrogenase {ECO:0000303|PubMed:12535615};
DE AltName: Full=L-allo-threonine dehydrogenase {ECO:0000303|PubMed:12535615};
DE EC=1.1.1.- {ECO:0000269|PubMed:12535615};
DE EC=1.1.1.381 {ECO:0000269|PubMed:12535615};
GN OrderedLocusNames=YMR226C {ECO:0000312|SGD:S000004839};
GN ORFNames=YM9959.08C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP PROTEIN SEQUENCE OF 1-14, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP 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 [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [5]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH NADP.
RA Huether R., Pacheco C.M., Duax W.L.;
RT "Substrate fingerprint and the structure of NADP(+)-dependent serine
RT dehydrogenase from Saccharomyces cerevisiae complexed with NADP(+).";
RL Submitted (APR-2011) to the PDB data bank.
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. {ECO:0000269|PubMed:12535615}.
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 -!- CATALYTIC ACTIVITY:
CC Reaction=L-allo-threonine + NADP(+) = (2S)-2-amino-3-oxobutanoate +
CC H(+) + NADPH; Xref=Rhea:RHEA:30055, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:58585,
CC ChEBI:CHEBI:78948; Evidence={ECO:0000269|PubMed:12535615};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.5 mM for NADP(+) (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=95 mM for L-serine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=71 mM for D-serine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=7 mM for D-threonine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=3 mM for L-allo-threonine (at pH 9 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:12535615};
CC KM=36 mM for L-3-hydroxyisobutyrate (at pH 9 and at 30 degrees
CC Celsius) {ECO:0000269|PubMed:12535615};
CC KM=57 mM for D-3-hydroxyisobutyrate (at pH 9 and at 30 degrees
CC Celsius) {ECO:0000269|PubMed:12535615};
CC KM=95 mM for L-3-hydroxybutyrate (at pH 9 and at 30 degrees Celsius)
CC {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 7.5 to 10.5. {ECO:0000269|PubMed:12535615};
CC Temperature dependence:
CC Stable up to 40 degrees Celsius. {ECO:0000269|PubMed:12535615};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12535615}.
CC -!- INTERACTION:
CC Q05016; P39009: DUN1; NbExp=2; IntAct=EBI-27486, EBI-6194;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 3210 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR)
CC family. {ECO:0000305}.
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DR EMBL; Z49939; CAA90197.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10125.1; -; Genomic_DNA.
DR PIR; S57593; S57593.
DR RefSeq; NP_013953.1; NM_001182733.1.
DR PDB; 3RKU; X-ray; 2.60 A; A/B/C/D=1-267.
DR PDBsum; 3RKU; -.
DR AlphaFoldDB; Q05016; -.
DR SMR; Q05016; -.
DR BioGRID; 35404; 102.
DR DIP; DIP-1671N; -.
DR IntAct; Q05016; 14.
DR MINT; Q05016; -.
DR STRING; 4932.YMR226C; -.
DR iPTMnet; Q05016; -.
DR MaxQB; Q05016; -.
DR PaxDb; Q05016; -.
DR PRIDE; Q05016; -.
DR TopDownProteomics; Q05016; -.
DR DNASU; 855266; -.
DR EnsemblFungi; YMR226C_mRNA; YMR226C; YMR226C.
DR GeneID; 855266; -.
DR KEGG; sce:YMR226C; -.
DR SGD; S000004839; YMR226C.
DR VEuPathDB; FungiDB:YMR226C; -.
DR eggNOG; KOG1205; Eukaryota.
DR GeneTree; ENSGT00940000175996; -.
DR HOGENOM; CLU_010194_2_10_1; -.
DR InParanoid; Q05016; -.
DR OMA; WRWMWET; -.
DR BioCyc; YEAST:G3O-32907-MON; -.
DR BRENDA; 1.1.1.381; 984.
DR PRO; PR:Q05016; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q05016; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0004090; F:carbonyl reductase (NADPH) activity; IDA:SGD.
DR GO; GO:0016491; F:oxidoreductase activity; IDA:SGD.
DR GO; GO:0031132; F:serine 3-dehydrogenase activity; IDA:SGD.
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 3D-structure; Cytoplasm; Direct protein sequencing; NADP; Nucleus;
KW Oxidoreductase; Phosphoprotein; Reference proteome.
FT CHAIN 1..267
FT /note="NADP-dependent 3-hydroxy acid dehydrogenase"
FT /id="PRO_0000054873"
FT ACT_SITE 168
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10001"
FT BINDING 20..25
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 48..49
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 75..76
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 102
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 155
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 168
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 172
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 198..205
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|Ref.7"
FT MOD_RES 260
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT HELIX 5..11
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 15..20
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 24..36
FT /evidence="ECO:0007829|PDB:3RKU"
FT TURN 37..39
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 41..48
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 50..63
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 68..73
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 82..87
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 91..93
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 117..127
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 129..145
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 156..158
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 166..185
FT /evidence="ECO:0007829|PDB:3RKU"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 192..199
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 205..209
FT /evidence="ECO:0007829|PDB:3RKU"
FT TURN 210..212
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 214..221
FT /evidence="ECO:0007829|PDB:3RKU"
FT HELIX 229..240
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 246..255
FT /evidence="ECO:0007829|PDB:3RKU"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:3RKU"
SQ SEQUENCE 267 AA; 29158 MW; 77FCD713F724A9D7 CRC64;
MSQGRKAAER LAKKTVLITG ASAGIGKATA LEYLEASNGD MKLILAARRL EKLEELKKTI
DQEFPNAKVH VAQLDITQAE KIKPFIENLP QEFKDIDILV NNAGKALGSD RVGQIATEDI
QDVFDTNVTA LINITQAVLP IFQAKNSGDI VNLGSIAGRD AYPTGSIYCA SKFAVGAFTD
SLRKELINTK IRVILIAPGL VETEFSLVRY RGNEEQAKNV YKDTTPLMAD DVADLIVYAT
SRKQNTVIAD TLIFPTNQAS PHHIFRG
