ID G7ILW0_MEDTR Unreviewed; 533 AA.
AC G7ILW0;
DT 25-JAN-2012, integrated into UniProtKB/TrEMBL.
DT 25-JAN-2012, sequence version 1.
DT 27-MAR-2024, entry version 83.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000256|RuleBase:RU000585};
DE EC=2.1.2.1 {ECO:0000256|RuleBase:RU000585};
GN Name=11445860 {ECO:0000313|EnsemblPlants:AES64087};
GN OrderedLocusNames=MTR_2g018290 {ECO:0000313|EMBL:AES64087.1};
GN ORFNames=MtrunA17_Chr2g0285171 {ECO:0000313|EMBL:RHN72206.1};
OS Medicago truncatula (Barrel medic) (Medicago tribuloides).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Trifolieae; Medicago.
OX NCBI_TaxID=3880 {ECO:0000313|EMBL:AES64087.1, ECO:0000313|Proteomes:UP000002051};
RN [1] {ECO:0000313|EMBL:AES64087.1, ECO:0000313|Proteomes:UP000002051}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=A17 {ECO:0000313|EMBL:AES64087.1}, and cv. Jemalong A17
RC {ECO:0000313|EnsemblPlants:AES64087,
RC ECO:0000313|Proteomes:UP000002051};
RX PubMed=22089132; DOI=10.1038/nature10625;
RA Young N.D., Debelle F., Oldroyd G.E., Geurts R., Cannon S.B., Udvardi M.K.,
RA Benedito V.A., Mayer K.F., Gouzy J., Schoof H., Van de Peer Y., Proost S.,
RA Cook D.R., Meyers B.C., Spannagl M., Cheung F., De Mita S.,
RA Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A.K., Murray J.D.,
RA Naoumkina M.A., Rosen B., Silverstein K.A., Tang H., Rombauts S.,
RA Zhao P.X., Zhou P., Barbe V., Bardou P., Bechner M., Bellec A., Berger A.,
RA Berges H., Bidwell S., Bisseling T., Choisne N., Couloux A., Denny R.,
RA Deshpande S., Dai X., Doyle J.J., Dudez A.M., Farmer A.D., Fouteau S.,
RA Franken C., Gibelin C., Gish J., Goldstein S., Gonzalez A.J., Green P.J.,
RA Hallab A., Hartog M., Hua A., Humphray S.J., Jeong D.H., Jing Y.,
RA Jocker A., Kenton S.M., Kim D.J., Klee K., Lai H., Lang C., Lin S.,
RA Macmil S.L., Magdelenat G., Matthews L., McCorrison J., Monaghan E.L.,
RA Mun J.H., Najar F.Z., Nicholson C., Noirot C., O'Bleness M., Paule C.R.,
RA Poulain J., Prion F., Qin B., Qu C., Retzel E.F., Riddle C., Sallet E.,
RA Samain S., Samson N., Sanders I., Saurat O., Scarpelli C., Schiex T.,
RA Segurens B., Severin A.J., Sherrier D.J., Shi R., Sims S., Singer S.R.,
RA Sinharoy S., Sterck L., Viollet A., Wang B.B., Wang K., Wang M., Wang X.,
RA Warfsmann J., Weissenbach J., White D.D., White J.D., Wiley G.B.,
RA Wincker P., Xing Y., Yang L., Yao Z., Ying F., Zhai J., Zhou L., Zuber A.,
RA Denarie J., Dixon R.A., May G.D., Schwartz D.C., Rogers J., Quetier F.,
RA Town C.D., Roe B.A.;
RT "The Medicago genome provides insight into the evolution of rhizobial
RT symbioses.";
RL Nature 480:520-524(2011).
RN [2] {ECO:0000313|EMBL:AES64087.1, ECO:0000313|Proteomes:UP000002051}
RP GENOME REANNOTATION.
RC STRAIN=A17 {ECO:0000313|EMBL:AES64087.1}, and cv. Jemalong A17
RC {ECO:0000313|EnsemblPlants:AES64087,
RC ECO:0000313|Proteomes:UP000002051};
RX PubMed=24767513; DOI=10.1186/1471-2164-15-312;
RA Tang H., Krishnakumar V., Bidwell S., Rosen B., Chan A., Zhou S.,
RA Gentzbittel L., Childs K.L., Yandell M., Gundlach H., Mayer K.F.,
RA Schwartz D.C., Town C.D.;
RT "An improved genome release (version Mt4.0) for the model legume Medicago
RT truncatula.";
RL BMC Genomics 15:312-312(2014).
RN [3] {ECO:0000313|EnsemblPlants:AES64087}
RP IDENTIFICATION.
RC STRAIN=cv. Jemalong A17 {ECO:0000313|EnsemblPlants:AES64087};
RG EnsemblPlants;
RL Submitted (APR-2015) to UniProtKB.
RN [4] {ECO:0007829|PDB:6CCZ, ECO:0007829|PDB:6CD0}
RP X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) OF 82-533.
RX PubMed=29868052; DOI=10.3389/fpls.2018.00584;
RA Ruszkowski M., Sekula B., Ruszkowska A., Dauter Z.;
RT "Chloroplastic Serine Hydroxymethyltransferase From <i>Medicago
RT truncatula</i>: A Structural Characterization.";
RL Front. Plant Sci. 9:584-584(2018).
RN [5] {ECO:0000313|Proteomes:UP000265566}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Jemalong A17 {ECO:0000313|Proteomes:UP000265566};
RX PubMed=30397259; DOI=10.1038/s41477-018-0286-7;
RA Pecrix Y., Staton S.E., Sallet E., Lelandais-Briere C., Moreau S.,
RA Carrere S., Blein T., Jardinaud M.F., Latrasse D., Zouine M., Zahm M.,
RA Kreplak J., Mayjonade B., Satge C., Perez M., Cauet S., Marande W.,
RA Chantry-Darmon C., Lopez-Roques C., Bouchez O., Berard A., Debelle F.,
RA Munos S., Bendahmane A., Berges H., Niebel A., Buitink J., Frugier F.,
RA Benhamed M., Crespi M., Gouzy J., Gamas P.;
RT "Whole-genome landscape of Medicago truncatula symbiotic genes.";
RL Nat. Plants 4:1017-1025(2018).
RN [6] {ECO:0000313|EMBL:RHN72206.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Leaves {ECO:0000313|EMBL:RHN72206.1};
RA Pecrix Y., Gamas P., Carrere S.;
RT "Whole-genome landscape of Medicago truncatula symbiotic genes.";
RL Nat. Plants 0:0-0(2018).
CC -!- FUNCTION: Interconversion of serine and glycine.
CC {ECO:0000256|RuleBase:RU000585}.
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:0000256|RuleBase:RU000585};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|PIRSR:PIRSR000412-50, ECO:0000256|RuleBase:RU000585};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000256|ARBA:ARBA00004777, ECO:0000256|RuleBase:RU000585}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000256|ARBA:ARBA00006376,
CC ECO:0000256|RuleBase:RU000585}.
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DR EMBL; CM001218; AES64087.1; -; Genomic_DNA.
DR EMBL; PSQE01000002; RHN72206.1; -; Genomic_DNA.
DR RefSeq; XP_003593836.1; XM_003593788.2.
DR PDB; 6CCZ; X-ray; 2.14 A; A/B=82-533.
DR PDB; 6CD0; X-ray; 1.74 A; A/B/C/D=82-533.
DR PDB; 6CD1; X-ray; 1.91 A; A/B/C/D/E/F/G/H=82-533.
DR PDBsum; 6CCZ; -.
DR PDBsum; 6CD0; -.
DR PDBsum; 6CD1; -.
DR AlphaFoldDB; G7ILW0; -.
DR SMR; G7ILW0; -.
DR STRING; 3880.G7ILW0; -.
DR PaxDb; 3880-AES64087; -.
DR ProMEX; G7ILW0; -.
DR EnsemblPlants; AES64087; AES64087; MTR_2g018290.
DR GeneID; 11445860; -.
DR Gramene; AES64087; AES64087; MTR_2g018290.
DR KEGG; mtr:11445860; -.
DR eggNOG; KOG2467; Eukaryota.
DR HOGENOM; CLU_022477_0_1_1; -.
DR OMA; SRQKHFI; -.
DR OrthoDB; 5358603at2759; -.
DR BRENDA; 2.1.2.1; 3201.
DR UniPathway; UPA00193; -.
DR Proteomes; UP000002051; Chromosome 2.
DR Proteomes; UP000265566; Chromosome 2.
DR ExpressionAtlas; G7ILW0; differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IBA:GO_Central.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
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:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0006730; P:one-carbon metabolic process; IBA:GO_Central.
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:SF63; SERINE HYDROXYMETHYLTRANSFERASE 3, CHLOROPLASTIC; 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 3D-structure {ECO:0007829|PDB:6CCZ, ECO:0007829|PDB:6CD0};
KW Methyltransferase {ECO:0000313|EMBL:RHN72206.1};
KW One-carbon metabolism {ECO:0000256|ARBA:ARBA00022563,
KW ECO:0000256|RuleBase:RU000585};
KW Pyridoxal phosphate {ECO:0000256|ARBA:ARBA00022898,
KW ECO:0000256|PIRSR:PIRSR000412-50};
KW Reference proteome {ECO:0000313|Proteomes:UP000002051};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|RuleBase:RU000585}.
FT DOMAIN 87..477
FT /note="Serine hydroxymethyltransferase-like"
FT /evidence="ECO:0000259|Pfam:PF00464"
FT MOD_RES 318
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR000412-50"
SQ SEQUENCE 533 AA; 57664 MW; FA6DED10D5A34F34 CRC64;
MPAACSGVAS MIGYLQQPPL SSTKLHNFSH GGLLPQLHFN NNNHFKPCCK VSIHEATFGK
SSSSSSSPSS LPKKIGGDGS SFLDYGLSEA DPDVHAIINK EKDRQFRSLE LIASENFTSK
AVMEAVGSCL TNKYSEGLPG KRYYGGNEHI DELEILCQQR ALAAFHLDGD KWGVNVQPLS
GSPANFAVYT AILKPHDRIM GLDLPHGGHL SHGFMTAKRR VSGTSIYFES MPYRLDESTG
VIDYDMLEKT AALFRPKLII AGASAYPRDI DYARFRKIAD SVGAFLMMDM AHVSGLIAAS
VLADPFEFVD IVTTTTHKSL RGPRGGMIFF KKDAVHGVDL ESAINNAVFP GLQGGPHNHT
IGGLAVCLKY AQSPDFKNYQ NQVVANCRAL ANRLVEHEYK LVSGGSDNHL VLVDLRPSGI
DGARVEKILD MASITLNKNS VPGDKSALVP GGIRIGSPAM TTRGLGEKEF ELIADLIHEG
VRISLEAKSL VSGTKVQDFL NFVLAPEFPL GDKVSNLRRK VEALATQYPI PGV
//
