GLYP3_ARATH
ID GLYP3_ARATH Reviewed; 529 AA.
AC Q94JQ3; F4JUC7; Q9SUU0;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2013, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Serine hydroxymethyltransferase 3, chloroplastic {ECO:0000303|PubMed:10806255, ECO:0000303|PubMed:12730263};
DE Short=AtSHM3 {ECO:0000303|PubMed:12730263};
DE Short=AtSHMT3 {ECO:0000303|PubMed:20518745};
DE EC=2.1.2.1 {ECO:0000269|PubMed:20518745};
DE AltName: Full=Glycine hydroxymethyltransferase 3 {ECO:0000303|PubMed:20518745};
DE AltName: Full=Serine methylase 3 {ECO:0000303|PubMed:20518745};
DE Flags: Precursor;
GN Name=SHM3 {ECO:0000303|PubMed:10806255, ECO:0000303|PubMed:12730263};
GN Synonyms=SHMT3 {ECO:0000303|PubMed:20518745};
GN OrderedLocusNames=At4g32520 {ECO:0000312|Araport:AT4G32520};
GN ORFNames=F8B4.220 {ECO:0000312|EMBL:CAA22579.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
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 [5]
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 [6]
RP GENE FAMILY, FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP CATALYTIC ACTIVITY, PATHWAY, AND ACTIVITY REGULATION.
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 and
CC directs the hydroxymethyl moiety of serine into the metabolic network
CC of H4PteGlu(n)-bound one-carbon units. {ECO:0000269|PubMed:20518745}.
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:0000269|PubMed:20518745};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250|UniProtKB:P34896};
CC -!- ACTIVITY REGULATION: Inhibited by 5-CH3-H4PteGlu1/5 and 5-HCO-
CC H4PteGlu1/5 in vitro. {ECO:0000269|PubMed:20518745}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=217.7 uM for H4PteGlu1 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=13.3 uM for H4PteGlu2 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=3.06 uM for H4PteGlu3 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=0.83 uM for H4PteGlu4 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=0.64 uM for H4PteGlu5 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=0.69 uM for H4PteGlu6 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=0.67 uM for H4PteGlu7 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC KM=0.55 uM for H4PteGlu8 (at pH 8.5) {ECO:0000269|PubMed:20518745};
CC Note=kcat is 15.8 sec(-1) with H4PteGlu1 as substrate (at pH 8.5)
CC (PubMed:20518745). kcat is 7.6 sec(-1) with H4PteGlu2 as substrate
CC (at pH 8.5) (PubMed:20518745). kcat is 8.7 sec(-1) with H4PteGlu3 as
CC substrate (at pH 8.5) (PubMed:20518745). kcat is 4.3 sec(-1) with
CC H4PteGlu4 as substrate (at pH 8.5) (PubMed:20518745). kcat is 3.5
CC sec(-1) with H4PteGlu5 as substrate (at pH 8.5) (PubMed:20518745).
CC kcat is 3.5 sec(-1) with H4PteGlu6 as substrate (at pH 8.5)
CC (PubMed:20518745). kcat is 3.8 sec(-1) with H4PteGlu7 as substrate
CC (at pH 8.5) (PubMed:20518745). kcat is 3.3 sec(-1) with H4PteGlu8 as
CC substrate (at pH 8.5) (PubMed:20518745).
CC {ECO:0000269|PubMed:20518745};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000269|PubMed:20518745}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:P34896}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:20518745}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA22579.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79969.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL034567; CAA22579.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161581; CAB79969.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86071.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86072.1; -; Genomic_DNA.
DR EMBL; AF375450; AAK53034.1; -; mRNA.
DR EMBL; BT000641; AAN18207.1; -; mRNA.
DR PIR; T05362; T05362.
DR RefSeq; NP_001119098.1; NM_001125626.1.
DR RefSeq; NP_567895.1; NM_119404.3.
DR AlphaFoldDB; Q94JQ3; -.
DR SMR; Q94JQ3; -.
DR BioGRID; 14673; 6.
DR IntAct; Q94JQ3; 3.
DR STRING; 3702.AT4G32520.1; -.
DR iPTMnet; Q94JQ3; -.
DR PaxDb; Q94JQ3; -.
DR PRIDE; Q94JQ3; -.
DR ProteomicsDB; 248545; -.
DR EnsemblPlants; AT4G32520.1; AT4G32520.1; AT4G32520.
DR EnsemblPlants; AT4G32520.2; AT4G32520.2; AT4G32520.
DR GeneID; 829387; -.
DR Gramene; AT4G32520.1; AT4G32520.1; AT4G32520.
DR Gramene; AT4G32520.2; AT4G32520.2; AT4G32520.
DR KEGG; ath:AT4G32520; -.
DR Araport; AT4G32520; -.
DR TAIR; locus:2127806; AT4G32520.
DR eggNOG; KOG2467; Eukaryota.
DR HOGENOM; CLU_022477_0_1_1; -.
DR InParanoid; Q94JQ3; -.
DR OMA; QACAISC; -.
DR OrthoDB; 372408at2759; -.
DR BioCyc; ARA:AT4G32520-MON; -.
DR BRENDA; 2.1.2.1; 399.
DR SABIO-RK; Q94JQ3; -.
DR UniPathway; UPA00193; -.
DR PRO; PR:Q94JQ3; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94JQ3; baseline and differential.
DR Genevisible; Q94JQ3; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IDA:TAIR.
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: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 1: Evidence at protein level;
KW Chloroplast; One-carbon metabolism; Plastid; Pyridoxal phosphate;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..60
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 61..529
FT /note="Serine hydroxymethyltransferase 3, chloroplastic"
FT /id="PRO_0000422348"
FT MOD_RES 314
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:P34896"
FT CONFLICT 514
FT /note="K -> T (in Ref. 3; AAK53034/AAN18207)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 529 AA; 57983 MW; 0DACD71EFDB8D8C7 CRC64;
MQACCGGNSM ASLQQPGRVQ GSVFPPIMPP VTKFSQQLKF NISKPFRSSF LKRNLVSEMR
ASSVSLPNVE ISSKEIPFED YGLGEVDPEV RTIITKEKDR QFRSLELIAS ENFTSRAVME
AVGSCLTNKY SEGLPGKRYY GGNEYIDQLE TLCQNRALAA FRLDSTKWGV NVQPLSGSPA
NFAVYTAILS PHDRIMGLDL PHGGHLSHGF MTAKRRVSGT SIYFESMPYR LDESTGIVDY
DMLEKTATLF RPKLIIAGAS AYSRDFDYPR MRKIADSVGA FLMMDMAHIS GLVAASVVAD
PFEYCDIVTT TTHKSLRGPR GGMIFFRKDP INGVDLESAV NNAVFPGLQG GPHNHTIGGL
AVCLKHAQSP EFKAYQKRVV SNCRALANRL VELGFKLVSG GSDNHLVLVD LRPMGMDGAR
VEKILDMASI TLNKNSVPGD KSALVPGGIR IGSPAMTTRG LSEKDFVVVA DFIKEGVEIT
MEAKKAAPGS KLQDFNKFVT SPEFPLKERV KSLKERVETF TSRFPIPGV
