GLYC5_ARATH
ID GLYC5_ARATH Reviewed; 470 AA.
AC Q9SVM4;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Serine hydroxymethyltransferase 5;
DE Short=AtSHMT5;
DE EC=2.1.2.1;
DE AltName: Full=Glycine hydroxymethyltransferase 5;
DE AltName: Full=Protein EMBRYO SAC DEVELOPMENT ARREST 36;
DE AltName: Full=Protein EMBRYO SAC DEVELOPMENT ARREST 37;
DE AltName: Full=Serine methylase 5;
GN Name=SHM5; Synonyms=EDA36, EDA37, SHMT5; OrderedLocusNames=At4g13890;
GN ORFNames=F18A5.280;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=10806255; DOI=10.1104/pp.123.1.381;
RA McClung C.R., Hsu M., Painter J.E., Gagne J.M., Karlsberg S.D.,
RA Salome P.A.;
RT "Integrated temporal regulation of the photorespiratory pathway. Circadian
RT regulation of two Arabidopsis genes encoding serine
RT hydroxymethyltransferase.";
RL Plant Physiol. 123:381-392(2000).
RN [4]
RP REVIEW.
RX PubMed=12730263; DOI=10.1093/jxb/erg171;
RA Bauwe H., Kolukisaoglu U.;
RT "Genetic manipulation of glycine decarboxylation.";
RL J. Exp. Bot. 54:1523-1535(2003).
RN [5]
RP GENE FAMILY.
RX PubMed=20518745; DOI=10.1042/bj20100566;
RA Zhang Y., Sun K., Sandoval F.J., Santiago K., Roje S.;
RT "One-carbon metabolism in plants: characterization of a plastid serine
RT hydroxymethyltransferase.";
RL Biochem. J. 430:97-105(2010).
CC -!- FUNCTION: Catalyzes the interconversion of serine and glycine.
CC {ECO:0000250}.
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 -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000305}.
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DR EMBL; AL035528; CAB36853.1; -; Genomic_DNA.
DR EMBL; AL161537; CAB78431.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83342.1; -; Genomic_DNA.
DR PIR; T05258; T05258.
DR RefSeq; NP_193125.1; NM_117463.3.
DR AlphaFoldDB; Q9SVM4; -.
DR SMR; Q9SVM4; -.
DR STRING; 3702.AT4G13890.1; -.
DR PaxDb; Q9SVM4; -.
DR PRIDE; Q9SVM4; -.
DR EnsemblPlants; AT4G13890.1; AT4G13890.1; AT4G13890.
DR GeneID; 827024; -.
DR Gramene; AT4G13890.1; AT4G13890.1; AT4G13890.
DR KEGG; ath:AT4G13890; -.
DR Araport; AT4G13890; -.
DR TAIR; locus:2119545; AT4G13890.
DR eggNOG; KOG2467; Eukaryota.
DR HOGENOM; CLU_022477_0_1_1; -.
DR InParanoid; Q9SVM4; -.
DR OMA; GRRYYEG; -.
DR OrthoDB; 372408at2759; -.
DR PhylomeDB; Q9SVM4; -.
DR BioCyc; ARA:AT4G13890-MON; -.
DR UniPathway; UPA00193; -.
DR PRO; PR:Q9SVM4; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SVM4; baseline and differential.
DR Genevisible; Q9SVM4; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0010197; P:polar nucleus fusion; IMP:TAIR.
DR GO; GO:0009555; P:pollen development; IMP:TAIR.
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; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 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; PTHR11680; 1.
DR Pfam; PF00464; SHMT; 1.
DR PIRSF; PIRSF000412; SHMT; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00096; SHMT; 1.
PE 3: Inferred from homology;
KW Cytoplasm; One-carbon metabolism; Pyridoxal phosphate; Reference proteome;
KW Transferase.
FT CHAIN 1..470
FT /note="Serine hydroxymethyltransferase 5"
FT /id="PRO_0000422350"
FT MOD_RES 244
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 470 AA; 52261 MW; A9949027F62FE732 CRC64;
MEPVYSWGNT HLDFVDPEIY DLIEKEKHRQ CRGIELIAAE NFTSVAVMEA LGSCLTNKYS
EGMPGNRYYG GTEFIDEIES LCRSRSLEAF HCNPEKWGVN VQPYSGSPAN FAAYTALLQP
HDRIMGLDLP SGGHITHGYY SSGGKNISAT SIYFENLPYK VDSKTGYIDY DKLEEKAMDF
RPKLIICGGT SYPREWDYAR FRAVADKVGA FLLCDMAHNS ALVAAQEAAD PFEYCDVVTT
STHKSLRGPR AGMIFYRKGP KPAKKGQPEG EVYDFDAKIN SAVFPALQSG PHNNKIGALA
VALKQVMAPS FKVYAKQVKA NAACLASYLI NKGYTLVTDG TDNHLILWDL RPLGLTGNKV
EKVCELCYIT LNRNAVFGDT SFLAPGGVRI GTPAMTSRGL VEKDFEKIGE FLHRAVTITL
DIQEQYGKVM KDFNKGLVNN KEIDEIKADV EEFTYDFDMP GFFISESRND
