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Protein

Serine hydroxymethyltransferase 1, mitochondrial

Gene

SHM1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Functions in the photorespiratory pathway in catalyzing the interconversion of serine and glycine. Involved in controlling cell damage caused by abiotic stress, such as high light and salt and the hypersensitive defense response of plants.4 Publications

Catalytic activityi

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.

Cofactori

Pathwayi: tetrahydrofolate interconversion

This protein is involved in the pathway tetrahydrofolate interconversion, which is part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the pathway tetrahydrofolate interconversion and in One-carbon metabolism.

GO - Molecular functioni

  • glycine hydroxymethyltransferase activity Source: UniProtKB
  • poly(U) RNA binding Source: TAIR
  • pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  • circadian rhythm Source: UniProtKB
  • glycine metabolic process Source: UniProtKB
  • L-serine metabolic process Source: UniProtKB
  • photorespiration Source: UniProtKB
  • plant-type hypersensitive response Source: TAIR
  • response to cadmium ion Source: TAIR
  • response to cold Source: TAIR
  • response to light stimulus Source: UniProtKB
  • tetrahydrofolate interconversion Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

One-carbon metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT4G37930-MONOMER.
MetaCyc:AT4G37930-MONOMER.
ReactomeiR-ATH-196757. Metabolism of folate and pterines.
R-ATH-71262. Carnitine synthesis.
UniPathwayiUPA00193.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferase 1, mitochondrial (EC:2.1.2.1)
Short name:
AtSHMT1
Alternative name(s):
Glycine hydroxymethyltransferase 1
Serine Transhydroxymethyltransferase
Short name:
STM
Serine methylase 1
Gene namesi
Name:SHM1
Synonyms:SHMT1, STM
Ordered Locus Names:At4g37930
ORF Names:F20D10.50
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G37930.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
  • chloroplast thylakoid Source: TAIR
  • cytosol Source: UniProtKB
  • cytosolic ribosome Source: TAIR
  • membrane Source: TAIR
  • mitochondrial matrix Source: TAIR
  • mitochondrion Source: UniProtKB
  • nucleus Source: TAIR
  • plasma membrane Source: TAIR
  • stromule Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Disruption phenotypei

Displays a lethal photorespiratory phenotype when grown at ambient carbon dioxide.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3030MitochondrionBy similarityAdd
BLAST
Chaini31 – 517487Serine hydroxymethyltransferase 1, mitochondrialPRO_0000032569Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei286 – 2861N6-(pyridoxal phosphate)lysineBy similarity

Post-translational modificationi

Ubiquitinated.1 Publication

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiQ9SZJ5.
PRIDEiQ9SZJ5.

PTM databases

iPTMnetiQ9SZJ5.

Expressioni

Tissue specificityi

Ubiquitous. Mostly expressed in leaves, less abundant in stems, flowers and siliques, and barely detectable in roots.4 Publications

Inductioni

Circadian-regulation. Induction by light.1 Publication

Gene expression databases

GenevisibleiQ9SZJ5. AT.

Interactioni

Subunit structurei

Homotetramer (By similarity). Interacts with GLU1. Interacts with UBP16.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GLU1Q9ZNZ72EBI-2292536,EBI-2292564
UBP16Q9SB513EBI-2292536,EBI-6589403

Protein-protein interaction databases

BioGridi15230. 5 interactions.
IntActiQ9SZJ5. 2 interactions.
STRINGi3702.AT4G37930.1.

Structurei

3D structure databases

ProteinModelPortaliQ9SZJ5.
SMRiQ9SZJ5. Positions 55-510.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SHMT family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
HOGENOMiHOG000239405.
InParanoidiQ9SZJ5.
KOiK00600.
OMAiMTIANYD.
PhylomeDBiQ9SZJ5.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9SZJ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMAMALRRL SSSIDKPIRP LIRSTSCYMS SLPSEAVDEK ERSRVTWPKQ
60 70 80 90 100
LNAPLEEVDP EIADIIEHEK ARQWKGLELI PSENFTSVSV MQAVGSVMTN
110 120 130 140 150
KYSEGYPGAR YYGGNEYIDM AETLCQKRAL EAFRLDPEKW GVNVQPLSGS
160 170 180 190 200
PANFHVYTAL LKPHERIMAL DLPHGGHLSH GYQTDTKKIS AVSIFFETMP
210 220 230 240 250
YRLDESTGYI DYDQMEKSAT LFRPKLIVAG ASAYARLYDY ARIRKVCNKQ
260 270 280 290 300
KAVMLADMAH ISGLVAANVI PSPFDYADVV TTTTHKSLRG PRGAMIFFRK
310 320 330 340 350
GVKEINKQGK EVLYDFEDKI NQAVFPGLQG GPHNHTITGL AVALKQATTS
360 370 380 390 400
EYKAYQEQVL SNSAKFAQTL MERGYELVSG GTDNHLVLVN LKPKGIDGSR
410 420 430 440 450
VEKVLEAVHI ASNKNTVPGD VSAMVPGGIR MGTPALTSRG FVEEDFAKVA
460 470 480 490 500
EYFDKAVTIA LKVKSEAQGT KLKDFVSAME SSSTIQSEIA KLRHEVEEFA
510
KQFPTIGFEK ETMKYKN
Length:517
Mass (Da):57,401
Last modified:May 1, 2000 - v1
Checksum:i5FDB9F6085B8B19F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti171 – 1711D → N in AAL06913 (PubMed:14593172).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ271726 mRNA. Translation: CAB71289.1.
AL035538 Genomic DNA. Translation: CAB37533.1.
AL161592 Genomic DNA. Translation: CAB80458.1.
CP002687 Genomic DNA. Translation: AEE86855.1.
AF428388 mRNA. Translation: AAL16156.1.
AY054254 mRNA. Translation: AAL06913.1.
AY057645 mRNA. Translation: AAL15276.1.
AY070726 mRNA. Translation: AAL50068.1.
BT006353 mRNA. Translation: AAP21161.1.
PIRiT05620.
RefSeqiNP_195506.1. NM_119954.3.
UniGeneiAt.21766.

Genome annotation databases

EnsemblPlantsiAT4G37930.1; AT4G37930.1; AT4G37930.
GeneIDi829949.
GrameneiAT4G37930.1; AT4G37930.1; AT4G37930.
KEGGiath:AT4G37930.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ271726 mRNA. Translation: CAB71289.1.
AL035538 Genomic DNA. Translation: CAB37533.1.
AL161592 Genomic DNA. Translation: CAB80458.1.
CP002687 Genomic DNA. Translation: AEE86855.1.
AF428388 mRNA. Translation: AAL16156.1.
AY054254 mRNA. Translation: AAL06913.1.
AY057645 mRNA. Translation: AAL15276.1.
AY070726 mRNA. Translation: AAL50068.1.
BT006353 mRNA. Translation: AAP21161.1.
PIRiT05620.
RefSeqiNP_195506.1. NM_119954.3.
UniGeneiAt.21766.

3D structure databases

ProteinModelPortaliQ9SZJ5.
SMRiQ9SZJ5. Positions 55-510.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15230. 5 interactions.
IntActiQ9SZJ5. 2 interactions.
STRINGi3702.AT4G37930.1.

PTM databases

iPTMnetiQ9SZJ5.

Proteomic databases

PaxDbiQ9SZJ5.
PRIDEiQ9SZJ5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G37930.1; AT4G37930.1; AT4G37930.
GeneIDi829949.
GrameneiAT4G37930.1; AT4G37930.1; AT4G37930.
KEGGiath:AT4G37930.

Organism-specific databases

TAIRiAT4G37930.

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
HOGENOMiHOG000239405.
InParanoidiQ9SZJ5.
KOiK00600.
OMAiMTIANYD.
PhylomeDBiQ9SZJ5.

Enzyme and pathway databases

UniPathwayiUPA00193.
BioCyciARA:AT4G37930-MONOMER.
MetaCyc:AT4G37930-MONOMER.
ReactomeiR-ATH-196757. Metabolism of folate and pterines.
R-ATH-71262. Carnitine synthesis.

Miscellaneous databases

PROiQ9SZJ5.

Gene expression databases

GenevisibleiQ9SZJ5. AT.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Photosynthesis and fluorescence quenching, and the mRNA levels of plastidic glutamine synthetase or of mitochondrial serine hydroxymethyltransferase (SHMT) in the leaves of the wild-type and of the SHMT-deficient stm mutant of Arabidopsis thaliana in relation to the rate of photorespiration."
    Beckmann K., Dzuibany C., Biehler K., Fock H., Hell R., Migge A., Becker T.W.
    Planta 202:379-386(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Integrated temporal regulation of the photorespiratory pathway. Circadian regulation of two Arabidopsis genes encoding serine hydroxymethyltransferase."
    McClung C.R., Hsu M., Painter J.E., Gagne J.M., Karlsberg S.D., Salome P.A.
    Plant Physiol. 123:381-392(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE, INDUCTION, TISSUE SPECIFICITY.
  6. "Genetic manipulation of glycine decarboxylation."
    Bauwe H., Kolukisaoglu U.
    J. Exp. Bot. 54:1523-1535(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  7. "Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins."
    Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H.
    Plant Cell 16:241-256(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Landsberg erecta.
  8. "Arabidopsis SHMT1, a serine hydroxymethyltransferase that functions in the photorespiratory pathway influences resistance to biotic and abiotic stress."
    Moreno J.I., Martin R., Castresana C.
    Plant J. 41:451-463(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
  9. "The photorespiratory Arabidopsis shm1 mutant is deficient in SHM1."
    Voll L.M., Jamai A., Renne P., Voll H., McClung C.R., Weber A.P.
    Plant Physiol. 140:59-66(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
  10. "Arabidopsis photorespiratory serine hydroxymethyltransferase activity requires the mitochondrial accumulation of ferredoxin-dependent glutamate synthase."
    Jamai A., Salome P.A., Schilling S.H., Weber A.P., McClung C.R.
    Plant Cell 21:595-606(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GLU1.
  11. "One-carbon metabolism in plants: characterization of a plastid serine hydroxymethyltransferase."
    Zhang Y., Sun K., Sandoval F.J., Santiago K., Roje S.
    Biochem. J. 430:97-105(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.
  12. "The presequence of Arabidopsis serine hydroxymethyltransferase SHM2 selectively prevents import into mesophyll mitochondria."
    Engel N., Ewald R., Gupta K.J., Zrenner R., Hagemann M., Bauwe H.
    Plant Physiol. 157:1711-1720(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, FUNCTION.
  13. "Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability."
    Zhou H., Zhao J., Yang Y., Chen C., Liu Y., Jin X., Chen L., Li X., Deng X.W., Schumaker K.S., Guo Y.
    Plant Cell 24:5106-5122(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH UBP16, SUBCELLULAR LOCATION, UBIQUITINATION, FUNCTION.

Entry informationi

Entry nameiGLYM1_ARATH
AccessioniPrimary (citable) accession number: Q9SZJ5
Secondary accession number(s): Q940M9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: May 1, 2000
Last modified: February 17, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Recessive mutant shmt1-1 (shm1-3) shows enhanced susceptibility to salt stress and to biotrophic and necrotrophic pathogens.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.