GLYM1_ARATH
ID GLYM1_ARATH Reviewed; 517 AA.
AC Q9SZJ5; Q940M9;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Serine hydroxymethyltransferase 1, mitochondrial {ECO:0000303|PubMed:10806255};
DE Short=AtSHMT1 {ECO:0000303|PubMed:15659103};
DE EC=2.1.2.1 {ECO:0000269|PubMed:21976482};
DE AltName: Full=Glycine hydroxymethyltransferase 1 {ECO:0000305};
DE AltName: Full=Serine Transhydroxymethyltransferase {ECO:0000305};
DE Short=STM {ECO:0000305};
DE AltName: Full=Serine methylase 1 {ECO:0000305};
DE Flags: Precursor;
GN Name=SHM1 {ECO:0000303|PubMed:10806255};
GN Synonyms=SHMT1 {ECO:0000303|PubMed:15659103}, STM {ECO:0000305};
GN OrderedLocusNames=At4g37930 {ECO:0000312|Araport:AT4G37930};
GN ORFNames=F20D10.50 {ECO:0000312|EMBL:CAB37533.1};
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 [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=9232907; DOI=10.1007/s004250050140;
RA Beckmann K., Dzuibany C., Biehler K., Fock H., Hell R., Migge A.,
RA Becker T.W.;
RT "Photosynthesis and fluorescence quenching, and the mRNA levels of
RT plastidic glutamine synthetase or of mitochondrial serine
RT hydroxymethyltransferase (SHMT) in the leaves of the wild-type and of the
RT SHMT-deficient stm mutant of Arabidopsis thaliana in relation to the rate
RT of photorespiration.";
RL Planta 202:379-386(1997).
RN [2]
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 [3]
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 [4]
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 [5]
RP GENE FAMILY, NOMENCLATURE, INDUCTION, AND TISSUE SPECIFICITY.
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 [6]
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 [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=15659103; DOI=10.1111/j.1365-313x.2004.02311.x;
RA Moreno J.I., Martin R., Castresana C.;
RT "Arabidopsis SHMT1, a serine hydroxymethyltransferase that functions in the
RT photorespiratory pathway influences resistance to biotic and abiotic
RT stress.";
RL Plant J. 41:451-463(2005).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=16339799; DOI=10.1104/pp.105.071399;
RA Voll L.M., Jamai A., Renne P., Voll H., McClung C.R., Weber A.P.;
RT "The photorespiratory Arabidopsis shm1 mutant is deficient in SHM1.";
RL Plant Physiol. 140:59-66(2006).
RN [10]
RP INTERACTION WITH GLU1.
RX PubMed=19223513; DOI=10.1105/tpc.108.063289;
RA Jamai A., Salome P.A., Schilling S.H., Weber A.P., McClung C.R.;
RT "Arabidopsis photorespiratory serine hydroxymethyltransferase activity
RT requires the mitochondrial accumulation of ferredoxin-dependent glutamate
RT synthase.";
RL Plant Cell 21:595-606(2009).
RN [11]
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).
RN [12]
RP CATALYTIC ACTIVITY, TISSUE SPECIFICITY, AND FUNCTION.
RX PubMed=21976482; DOI=10.1104/pp.111.184564;
RA Engel N., Ewald R., Gupta K.J., Zrenner R., Hagemann M., Bauwe H.;
RT "The presequence of Arabidopsis serine hydroxymethyltransferase SHM2
RT selectively prevents import into mesophyll mitochondria.";
RL Plant Physiol. 157:1711-1720(2011).
RN [13]
RP INTERACTION WITH UBP16, SUBCELLULAR LOCATION, UBIQUITINATION, AND FUNCTION.
RX PubMed=23232097; DOI=10.1105/tpc.112.106393;
RA Zhou H., Zhao J., Yang Y., Chen C., Liu Y., Jin X., Chen L., Li X.,
RA Deng X.W., Schumaker K.S., Guo Y.;
RT "Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by
RT regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase
RT stability.";
RL Plant Cell 24:5106-5122(2012).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP SER-30.
RX PubMed=25862457; DOI=10.1104/pp.15.00300;
RA Huang S., Nelson C.J., Li L., Taylor N.L., Stroeher E., Peteriet J.,
RA Millar A.H.;
RT "INTERMEDIATE CLEAVAGE PEPTIDASE55 modifies enzyme amino termini and alters
RT protein stability in Arabidopsis mitochondria.";
RL Plant Physiol. 168:415-427(2015).
CC -!- FUNCTION: Functions in the photorespiratory pathway in catalyzing the
CC interconversion of serine and glycine. Involved in controlling cell
CC damage caused by abiotic stress, such as high light and salt and the
CC hypersensitive defense response of plants.
CC {ECO:0000269|PubMed:15659103, ECO:0000269|PubMed:16339799,
CC ECO:0000269|PubMed:21976482, ECO:0000269|PubMed:23232097}.
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:21976482};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250|UniProtKB:P34896};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer (By similarity). Interacts with GLU1
CC (PubMed:19223513). Interacts with UBP16 (PubMed:23232097).
CC {ECO:0000250|UniProtKB:P34896, ECO:0000269|PubMed:19223513,
CC ECO:0000269|PubMed:23232097}.
CC -!- INTERACTION:
CC Q9SZJ5; Q9ZNZ7: GLU1; NbExp=2; IntAct=EBI-2292536, EBI-2292564;
CC Q9SZJ5; Q9SB51: UBP16; NbExp=3; IntAct=EBI-2292536, EBI-6589403;
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305|PubMed:25862457}.
CC Cytoplasm.
CC -!- TISSUE SPECIFICITY: Ubiquitous. Mostly expressed in leaves, less
CC abundant in stems, flowers and siliques, and barely detectable in
CC roots. {ECO:0000269|PubMed:10806255, ECO:0000269|PubMed:15659103,
CC ECO:0000269|PubMed:16339799, ECO:0000269|PubMed:21976482}.
CC -!- INDUCTION: Circadian-regulation. Induction by light.
CC {ECO:0000269|PubMed:10806255}.
CC -!- PTM: Ubiquitinated. {ECO:0000269|PubMed:23232097}.
CC -!- DISRUPTION PHENOTYPE: Displays a lethal photorespiratory phenotype when
CC grown at ambient carbon dioxide. {ECO:0000269|PubMed:15659103,
CC ECO:0000269|PubMed:16339799}.
CC -!- MISCELLANEOUS: Recessive mutant shmt1-1 (shm1-3) shows enhanced
CC susceptibility to salt stress and to biotrophic and necrotrophic
CC pathogens. {ECO:0000305|PubMed:15659103}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000305}.
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DR EMBL; AJ271726; CAB71289.1; -; mRNA.
DR EMBL; AL035538; CAB37533.1; -; Genomic_DNA.
DR EMBL; AL161592; CAB80458.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86855.1; -; Genomic_DNA.
DR EMBL; AF428388; AAL16156.1; -; mRNA.
DR EMBL; AY054254; AAL06913.1; -; mRNA.
DR EMBL; AY057645; AAL15276.1; -; mRNA.
DR EMBL; AY070726; AAL50068.1; -; mRNA.
DR EMBL; BT006353; AAP21161.1; -; mRNA.
DR PIR; T05620; T05620.
DR RefSeq; NP_195506.1; NM_119954.4.
DR AlphaFoldDB; Q9SZJ5; -.
DR SMR; Q9SZJ5; -.
DR BioGRID; 15230; 15.
DR IntAct; Q9SZJ5; 2.
DR STRING; 3702.AT4G37930.1; -.
DR iPTMnet; Q9SZJ5; -.
DR PaxDb; Q9SZJ5; -.
DR PRIDE; Q9SZJ5; -.
DR ProteomicsDB; 248432; -.
DR EnsemblPlants; AT4G37930.1; AT4G37930.1; AT4G37930.
DR GeneID; 829949; -.
DR Gramene; AT4G37930.1; AT4G37930.1; AT4G37930.
DR KEGG; ath:AT4G37930; -.
DR Araport; AT4G37930; -.
DR TAIR; locus:2005518; AT4G37930.
DR eggNOG; KOG2467; Eukaryota.
DR HOGENOM; CLU_022477_0_1_1; -.
DR InParanoid; Q9SZJ5; -.
DR OMA; SHPAGLI; -.
DR OrthoDB; 372408at2759; -.
DR PhylomeDB; Q9SZJ5; -.
DR BioCyc; ARA:AT4G37930-MON; -.
DR BioCyc; MetaCyc:AT4G37930-MON; -.
DR UniPathway; UPA00193; -.
DR PRO; PR:Q9SZJ5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SZJ5; baseline and differential.
DR Genevisible; Q9SZJ5; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0022626; C:cytosolic ribosome; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; ISS:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0010319; C:stromule; IDA:TAIR.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IDA:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0008266; F:poly(U) RNA binding; 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:0007623; P:circadian rhythm; IEP:UniProtKB.
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:0006544; P:glycine metabolic process; IDA:UniProtKB.
DR GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR GO; GO:0006563; P:L-serine metabolic process; IDA:UniProtKB.
DR GO; GO:0006730; P:one-carbon metabolic process; IBA:GO_Central.
DR GO; GO:0009853; P:photorespiration; IMP:UniProtKB.
DR GO; GO:0009626; P:plant-type hypersensitive response; TAS:TAIR.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
DR GO; GO:0009416; P:response to light stimulus; IEP:UniProtKB.
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 Cytoplasm; Mitochondrion; One-carbon metabolism; Pyridoxal phosphate;
KW Reference proteome; Transferase; Transit peptide; Ubl conjugation.
FT TRANSIT 1..30
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25862457"
FT CHAIN 31..517
FT /note="Serine hydroxymethyltransferase 1, mitochondrial"
FT /id="PRO_0000032569"
FT MOD_RES 286
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:P34896"
FT CONFLICT 171
FT /note="D -> N (in Ref. 4; AAL06913)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 517 AA; 57401 MW; 5FDB9F6085B8B19F CRC64;
MAMAMALRRL SSSIDKPIRP LIRSTSCYMS SLPSEAVDEK ERSRVTWPKQ LNAPLEEVDP
EIADIIEHEK ARQWKGLELI PSENFTSVSV MQAVGSVMTN KYSEGYPGAR YYGGNEYIDM
AETLCQKRAL EAFRLDPEKW GVNVQPLSGS PANFHVYTAL LKPHERIMAL DLPHGGHLSH
GYQTDTKKIS AVSIFFETMP YRLDESTGYI DYDQMEKSAT LFRPKLIVAG ASAYARLYDY
ARIRKVCNKQ KAVMLADMAH ISGLVAANVI PSPFDYADVV TTTTHKSLRG PRGAMIFFRK
GVKEINKQGK EVLYDFEDKI NQAVFPGLQG GPHNHTITGL AVALKQATTS EYKAYQEQVL
SNSAKFAQTL MERGYELVSG GTDNHLVLVN LKPKGIDGSR VEKVLEAVHI ASNKNTVPGD
VSAMVPGGIR MGTPALTSRG FVEEDFAKVA EYFDKAVTIA LKVKSEAQGT KLKDFVSAME
SSSTIQSEIA KLRHEVEEFA KQFPTIGFEK ETMKYKN
