ID   GLYC_YEAST              Reviewed;         469 AA.
AC   P37291; D6VY60;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 2.
DT   27-MAR-2024, entry version 191.
DE   RecName: Full=Serine hydroxymethyltransferase, cytosolic {ECO:0000303|PubMed:8132653};
DE            Short=SHMT {ECO:0000303|PubMed:8132653};
DE            EC=2.1.2.1 {ECO:0000305|PubMed:8132653};
DE   AltName: Full=Glycine hydroxymethyltransferase;
DE   AltName: Full=Serine methylase;
GN   Name=SHM2 {ECO:0000303|PubMed:8132653}; Synonyms=SHMT2;
GN   OrderedLocusNames=YLR058C; ORFNames=L2156;
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 [GENOMIC DNA], AND FUNCTION.
RC   STRAIN=ATCC 201238 / W303-1B;
RX   PubMed=8132653; DOI=10.1016/s0021-9258(17)37089-8;
RA   McNeil J.B., McIntosh E.M., Taylor B.V., Zhang F.-R., Tang S., Bognar A.L.;
RT   "Cloning and molecular characterization of three genes, including two genes
RT   encoding serine hydroxymethyltransferases, whose inactivation is required
RT   to render yeast auxotrophic for glycine.";
RL   J. Biol. Chem. 269:9155-9165(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169871;
RA   Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA   Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA   Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA   Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA   Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA   Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA   Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA   Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA   Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA   Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA   Zollner A., Hani J., Hoheisel J.D.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL   Nature 387:87-90(1997).
RN   [3]
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   [4]
RP   PROTEIN SEQUENCE OF 151-161 AND 274-281.
RC   STRAIN=ATCC 44827 / SKQ2N;
RX   PubMed=9509572;
RX   DOI=10.1002/(sici)1097-0061(199712)13:16<1519::aid-yea211>3.0.co;2-u;
RA   Norbeck J., Blomberg A.;
RT   "Two-dimensional electrophoretic separation of yeast proteins using a non-
RT   linear wide range (pH 3-10) immobilized pH gradient in the first dimension;
RT   reproducibility and evidence for isoelectric focusing of alkaline (pI > 7)
RT   proteins.";
RL   Yeast 13:1519-1534(1997).
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-26 AND SER-429, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-20; SER-26 AND SER-429, AND
RP   IDENTIFICATION BY 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   [8]
RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-456, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22106047; DOI=10.1002/pmic.201100166;
RA   Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT   "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL   Proteomics 12:236-240(2012).
CC   -!- FUNCTION: Interconversion of serine and glycine.
CC       {ECO:0000305|PubMed:8132653}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O =
CC         (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384,
CC         ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
CC         Evidence={ECO:0000305|PubMed:8132653};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000250|UniProtKB:P34897};
CC   -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC       {ECO:0000305|PubMed:8132653}.
CC   -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:P34897}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:8132653}.
CC   -!- MISCELLANEOUS: In eukaryotes there are two forms of the enzymes: a
CC       cytosolic one and a mitochondrial one. {ECO:0000305|PubMed:8132653}.
CC   -!- MISCELLANEOUS: Present with 67600 molecules/cell in log phase SD
CC       medium. {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000305}.
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DR   EMBL; L22529; AAA21023.1; -; Genomic_DNA.
DR   EMBL; X94607; CAA64305.1; -; Genomic_DNA.
DR   EMBL; Z73230; CAA97588.1; -; Genomic_DNA.
DR   EMBL; BK006945; DAA09376.1; -; Genomic_DNA.
DR   PIR; S61632; S61632.
DR   RefSeq; NP_013159.1; NM_001181945.1.
DR   AlphaFoldDB; P37291; -.
DR   SMR; P37291; -.
DR   BioGRID; 31333; 163.
DR   DIP; DIP-2602N; -.
DR   IntAct; P37291; 25.
DR   MINT; P37291; -.
DR   STRING; 4932.YLR058C; -.
DR   iPTMnet; P37291; -.
DR   MaxQB; P37291; -.
DR   PaxDb; 4932-YLR058C; -.
DR   PeptideAtlas; P37291; -.
DR   EnsemblFungi; YLR058C_mRNA; YLR058C; YLR058C.
DR   GeneID; 850747; -.
DR   KEGG; sce:YLR058C; -.
DR   AGR; SGD:S000004048; -.
DR   SGD; S000004048; SHM2.
DR   VEuPathDB; FungiDB:YLR058C; -.
DR   eggNOG; KOG2467; Eukaryota.
DR   GeneTree; ENSGT00390000002762; -.
DR   HOGENOM; CLU_022477_0_1_1; -.
DR   InParanoid; P37291; -.
DR   OMA; CQFANVQ; -.
DR   OrthoDB; 5358603at2759; -.
DR   BioCyc; MetaCyc:YLR058C-MONOMER; -.
DR   BioCyc; YEAST:YLR058C-MONOMER; -.
DR   Reactome; R-SCE-196757; Metabolism of folate and pterines.
DR   Reactome; R-SCE-71262; Carnitine synthesis.
DR   UniPathway; UPA00193; -.
DR   BioGRID-ORCS; 850747; 1 hit in 10 CRISPR screens.
DR   PRO; PR:P37291; -.
DR   Proteomes; UP000002311; Chromosome XII.
DR   RNAct; P37291; Protein.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0043332; C:mating projection tip; HDA:SGD.
DR   GO; GO:0005886; C:plasma membrane; HDA:SGD.
DR   GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IMP:SGD.
DR   GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR   GO; GO:0070905; F:serine binding; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR   GO; GO:0046655; P:folic acid metabolic process; IBA:GO_Central.
DR   GO; GO:0019264; P:glycine biosynthetic process from serine; IBA:GO_Central.
DR   GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR   GO; GO:0006730; P:one-carbon metabolic process; IMP:SGD.
DR   GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR   GO; GO:0046653; P:tetrahydrofolate metabolic process; IBA:GO_Central.
DR   CDD; cd00378; SHMT; 1.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR   HAMAP; MF_00051; SHMT; 1.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR   InterPro; IPR001085; Ser_HO-MeTrfase.
DR   InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR   InterPro; IPR039429; SHMT-like_dom.
DR   PANTHER; PTHR11680; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR   PANTHER; PTHR11680:SF66; SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC; 1.
DR   Pfam; PF00464; SHMT; 1.
DR   PIRSF; PIRSF000412; SHMT; 1.
DR   SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR   PROSITE; PS00096; SHMT; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Direct protein sequencing; Isopeptide bond;
KW   One-carbon metabolism; Phosphoprotein; Pyridoxal phosphate;
KW   Reference proteome; Transferase; Ubl conjugation.
FT   CHAIN           1..469
FT                   /note="Serine hydroxymethyltransferase, cytosolic"
FT                   /id="PRO_0000113516"
FT   MOD_RES         20
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         26
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         248
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000250|UniProtKB:P34897"
FT   MOD_RES         429
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   CROSSLNK        456
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0007744|PubMed:22106047"
FT   CONFLICT        429
FT                   /note="S -> K (in Ref. 1; AAA21023)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   469 AA;  52218 MW;  4A79F79ED30A5965 CRC64;
     MPYTLSDAHH KLITSHLVDT DPEVDSIIKD EIERQKHSID LIASENFTST SVFDALGTPL
     SNKYSEGYPG ARYYGGNEHI DRMEILCQQR ALKAFHVTPD KWGVNVQTLS GSPANLQVYQ
     AIMKPHERLM GLYLPDGGHL SHGYATENRK ISAVSTYFES FPYRVNPETG IIDYDTLEKN
     AILYRPKVLV AGTSAYCRLI DYKRMREIAD KCGAYLMVDM AHISGLIAAG VIPSPFEYAD
     IVTTTTHKSL RGPRGAMIFF RRGVRSINPK TGKEVLYDLE NPINFSVFPG HQGGPHNHTI
     AALATALKQA ATPEFKEYQT QVLKNAKALE SEFKNLGYRL VSNGTDSHMV LVSLREKGVD
     GARVEYICEK INIALNKNSI PGDKSALVPG GVRIGAPAMT TRGMGEEDFH RIVQYINKAV
     EFAQQVQQSL PKDACRLKDF KAKVDEGSDV LNTWKKEIYD WAGEYPLAV
//