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Protein

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1

Gene

MS1

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

Functioni

Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation.1 Publication

Catalytic activityi

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine.

Cofactori

Zn2+Note: Binds 2 Zn2+ ions per subunit.

Kineticsi

  1. KM=60 µM for 5-methyltetrahydrofolate1 Publication
  1. Vmax=26.5 nmol/min/mg enzyme toward 5-methyltetrahydrofolate1 Publication

Pathwayi: L-methionine biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes L-methionine from L-homocysteine (MetE route).
Proteins known to be involved in this subpathway in this organism are:
  1. 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic (MS3), 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 2 (MS2), 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 (MS1)
This subpathway is part of the pathway L-methionine biosynthesis via de novo pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-methionine from L-homocysteine (MetE route), the pathway L-methionine biosynthesis via de novo pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei490 – 4901L-homocysteine
Binding sitei567 – 56715-methyltetrahydrofolate1 Publication
Binding sitei605 – 6051L-homocysteine
Metal bindingi647 – 6471Zinc 1
Metal bindingi649 – 6491Zinc 1
Metal bindingi658 – 6581Zinc 2
Metal bindingi662 – 6621Zinc 2
Metal bindingi733 – 7331Zinc 1

GO - Molecular functioni

  • 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity Source: GO_Central
  • copper ion binding Source: TAIR
  • methionine synthase activity Source: TAIR
  • zinc ion binding Source: UniProtKB

GO - Biological processi

  • homocysteine metabolic process Source: GO_Central
  • response to cadmium ion Source: TAIR
  • response to salt stress Source: TAIR
  • response to zinc ion Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Amino-acid biosynthesis, Methionine biosynthesis

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT5G17920-MONOMER.
ARA:GQT-1534-MONOMER.
BRENDAi2.1.1.14. 399.
SABIO-RKO50008.
UniPathwayiUPA00051; UER00082.

Names & Taxonomyi

Protein namesi
Recommended name:
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 (EC:2.1.1.14)
Alternative name(s):
Cobalamin-independent methionine synthase 1
Short name:
AtMS1
Vitamin-B12-independent methionine synthase 1
Gene namesi
Name:MS1
Synonyms:CIMS
Ordered Locus Names:At5g17920
ORF Names:MPI7.9
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G17920.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
  • cytosol Source: TAIR
  • membrane Source: TAIR
  • peroxisome Source: TAIR
  • plasma membrane Source: TAIR
  • plasmodesma Source: TAIR
  • vacuolar membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7657655-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1PRO_0000098696Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki406 – 406Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Post-translational modificationi

Ubiquitinated.1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiO50008.
PRIDEiO50008.

2D gel databases

SWISS-2DPAGEO50008.

PTM databases

iPTMnetiO50008.

Expressioni

Tissue specificityi

Expressed in leaves, stems, flowers, siliques and seeds.1 Publication

Gene expression databases

GenevisibleiO50008. AT.

Interactioni

Protein-protein interaction databases

BioGridi16936. 8 interactions.
IntActiO50008. 2 interactions.
STRINGi3702.AT5G17920.1.

Structurei

Secondary structure

1
765
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi16 – 2611Combined sources
Helixi31 – 5121Combined sources
Beta strandi58 – 603Combined sources
Helixi67 – 748Combined sources
Helixi80 – 823Combined sources
Beta strandi86 – 883Combined sources
Helixi91 – 999Combined sources
Beta strandi102 – 1043Combined sources
Beta strandi109 – 1113Combined sources
Beta strandi118 – 1203Combined sources
Helixi136 – 14611Combined sources
Beta strandi152 – 1565Combined sources
Helixi158 – 1636Combined sources
Beta strandi169 – 1713Combined sources
Helixi177 – 1804Combined sources
Helixi181 – 19717Combined sources
Beta strandi202 – 2065Combined sources
Helixi208 – 2114Combined sources
Helixi216 – 22813Combined sources
Turni230 – 2334Combined sources
Beta strandi235 – 2417Combined sources
Helixi249 – 2557Combined sources
Beta strandi263 – 2708Combined sources
Helixi274 – 2807Combined sources
Beta strandi287 – 2937Combined sources
Beta strandi295 – 2973Combined sources
Helixi303 – 31614Combined sources
Beta strandi322 – 3287Combined sources
Helixi330 – 3323Combined sources
Helixi337 – 3393Combined sources
Helixi345 – 3484Combined sources
Helixi354 – 36815Combined sources
Helixi374 – 38916Combined sources
Turni391 – 3933Combined sources
Helixi397 – 4004Combined sources
Turni401 – 4055Combined sources
Beta strandi411 – 4133Combined sources
Helixi416 – 4183Combined sources
Helixi420 – 4267Combined sources
Helixi463 – 47917Combined sources
Beta strandi484 – 4863Combined sources
Helixi498 – 5014Combined sources
Beta strandi504 – 5085Combined sources
Beta strandi515 – 5184Combined sources
Beta strandi521 – 5233Combined sources
Helixi541 – 5466Combined sources
Beta strandi554 – 5596Combined sources
Helixi561 – 5666Combined sources
Beta strandi568 – 5703Combined sources
Beta strandi572 – 5743Combined sources
Helixi576 – 59621Combined sources
Beta strandi601 – 6055Combined sources
Turni607 – 6126Combined sources
Helixi617 – 6193Combined sources
Helixi620 – 63516Combined sources
Beta strandi640 – 6478Combined sources
Turni654 – 6563Combined sources
Helixi657 – 6615Combined sources
Beta strandi666 – 6694Combined sources
Beta strandi672 – 6754Combined sources
Helixi679 – 6835Combined sources
Turni684 – 6874Combined sources
Beta strandi691 – 6933Combined sources
Beta strandi696 – 6983Combined sources
Beta strandi702 – 7043Combined sources
Helixi708 – 72013Combined sources
Beta strandi724 – 7274Combined sources
Beta strandi735 – 7384Combined sources
Helixi740 – 75920Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U1HX-ray2.55A1-765[»]
1U1JX-ray2.40A1-765[»]
1U1UX-ray2.95A1-765[»]
1U22X-ray2.65A1-765[»]
ProteinModelPortaliO50008.
SMRiO50008. Positions 2-760.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO50008.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni437 – 4393L-homocysteine binding
Regioni521 – 52225-methyltetrahydrofolate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2263. Eukaryota.
COG0620. LUCA.
HOGENOMiHOG000246221.
InParanoidiO50008.
KOiK00549.
OMAiRITNCEI.
PhylomeDBiO50008.

Family and domain databases

HAMAPiMF_00172. Meth_synth.
InterProiIPR013215. Cbl-indep_Met_Synth_N.
IPR006276. Cobalamin-indep_Met_synthase.
IPR002629. Met_Synth_C/arc.
[Graphical view]
PfamiPF08267. Meth_synt_1. 1 hit.
PF01717. Meth_synt_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000382. MeTrfase_B12_ind. 1 hit.
TIGRFAMsiTIGR01371. met_syn_B12ind. 1 hit.

Sequencei

Sequence statusi: Complete.

O50008-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASHIVGYPR MGPKRELKFA LESFWDGKST AEDLQKVSAD LRSSIWKQMS
60 70 80 90 100
AAGTKFIPSN TFAHYDQVLD TTAMLGAVPP RYGYTGGEIG LDVYFSMARG
110 120 130 140 150
NASVPAMEMT KWFDTNYHYI VPELGPEVNF SYASHKAVNE YKEAKALGVD
160 170 180 190 200
TVPVLVGPVS YLLLSKAAKG VDKSFELLSL LPKILPIYKE VITELKAAGA
210 220 230 240 250
TWIQLDEPVL VMDLEGQKLQ AFTGAYAELE STLSGLNVLV ETYFADIPAE
260 270 280 290 300
AYKTLTSLKG VTAFGFDLVR GTKTLDLVKA GFPEGKYLFA GVVDGRNIWA
310 320 330 340 350
NDFAASLSTL QALEGIVGKD KLVVSTSCSL LHTAVDLINE TKLDDEIKSW
360 370 380 390 400
LAFAAQKVVE VNALAKALAG QKDEALFSAN AAALASRRSS PRVTNEGVQK
410 420 430 440 450
AAAALKGSDH RRATNVSARL DAQQKKLNLP ILPTTTIGSF PQTVELRRVR
460 470 480 490 500
REYKAKKVSE EDYVKAIKEE IKKVVDLQEE LDIDVLVHGE PERNDMVEYF
510 520 530 540 550
GEQLSGFAFT ANGWVQSYGS RCVKPPVIYG DVSRPKAMTV FWSAMAQSMT
560 570 580 590 600
SRPMKGMLTG PVTILNWSFV RNDQPRHETC YQIALAIKDE VEDLEKGGIG
610 620 630 640 650
VIQIDEAALR EGLPLRKSEH AFYLDWAVHS FRITNCGVQD STQIHTHMCY
660 670 680 690 700
SHFNDIIHSI IDMDADVITI ENSRSDEKLL SVFREGVKYG AGIGPGVYDI
710 720 730 740 750
HSPRIPSSEE IADRVNKMLA VLEQNILWVN PDCGLKTRKY TEVKPALKNM
760
VDAAKLIRSQ LASAK
Length:765
Mass (Da):84,357
Last modified:June 1, 1998 - v1
Checksum:i2EA01908B5951154
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti270 – 2701R → L in AAL09712 (PubMed:14593172).Curated
Sequence conflicti282 – 2821F → S in CAE55863 (PubMed:15024005).Curated
Sequence conflicti295 – 2951G → R in AAN31836 (PubMed:14593172).Curated
Sequence conflicti351 – 3511L → M in CAE55863 (PubMed:15024005).Curated
Sequence conflicti442 – 4421Q → R in AAN31836 (PubMed:14593172).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U97200 mRNA. Translation: AAC50037.1.
AJ608673 mRNA. Translation: CAE55863.1.
AB011480 Genomic DNA. Translation: BAB11226.1.
CP002688 Genomic DNA. Translation: AED92486.1.
CP002688 Genomic DNA. Translation: AED92487.1.
AF370522 mRNA. Translation: AAK43899.1.
AY048201 mRNA. Translation: AAK82464.1.
AY056098 mRNA. Translation: AAL06986.1.
AY057478 mRNA. Translation: AAL09712.1.
AY057499 mRNA. Translation: AAL09740.1.
AY069876 mRNA. Translation: AAL47432.1.
AY070771 mRNA. Translation: AAL50108.1.
AY091692 mRNA. Translation: AAM10291.1.
BT000691 mRNA. Translation: AAN31836.1.
RefSeqiNP_001078599.1. NM_001085130.1.
NP_197294.1. NM_121798.3.
UniGeneiAt.22340.
At.24550.
At.71028.

Genome annotation databases

EnsemblPlantsiAT5G17920.1; AT5G17920.1; AT5G17920.
AT5G17920.2; AT5G17920.2; AT5G17920.
GeneIDi831660.
GrameneiAT5G17920.1; AT5G17920.1; AT5G17920.
AT5G17920.2; AT5G17920.2; AT5G17920.
KEGGiath:AT5G17920.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U97200 mRNA. Translation: AAC50037.1.
AJ608673 mRNA. Translation: CAE55863.1.
AB011480 Genomic DNA. Translation: BAB11226.1.
CP002688 Genomic DNA. Translation: AED92486.1.
CP002688 Genomic DNA. Translation: AED92487.1.
AF370522 mRNA. Translation: AAK43899.1.
AY048201 mRNA. Translation: AAK82464.1.
AY056098 mRNA. Translation: AAL06986.1.
AY057478 mRNA. Translation: AAL09712.1.
AY057499 mRNA. Translation: AAL09740.1.
AY069876 mRNA. Translation: AAL47432.1.
AY070771 mRNA. Translation: AAL50108.1.
AY091692 mRNA. Translation: AAM10291.1.
BT000691 mRNA. Translation: AAN31836.1.
RefSeqiNP_001078599.1. NM_001085130.1.
NP_197294.1. NM_121798.3.
UniGeneiAt.22340.
At.24550.
At.71028.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U1HX-ray2.55A1-765[»]
1U1JX-ray2.40A1-765[»]
1U1UX-ray2.95A1-765[»]
1U22X-ray2.65A1-765[»]
ProteinModelPortaliO50008.
SMRiO50008. Positions 2-760.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi16936. 8 interactions.
IntActiO50008. 2 interactions.
STRINGi3702.AT5G17920.1.

PTM databases

iPTMnetiO50008.

2D gel databases

SWISS-2DPAGEO50008.

Proteomic databases

PaxDbiO50008.
PRIDEiO50008.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G17920.1; AT5G17920.1; AT5G17920.
AT5G17920.2; AT5G17920.2; AT5G17920.
GeneIDi831660.
GrameneiAT5G17920.1; AT5G17920.1; AT5G17920.
AT5G17920.2; AT5G17920.2; AT5G17920.
KEGGiath:AT5G17920.

Organism-specific databases

TAIRiAT5G17920.

Phylogenomic databases

eggNOGiKOG2263. Eukaryota.
COG0620. LUCA.
HOGENOMiHOG000246221.
InParanoidiO50008.
KOiK00549.
OMAiRITNCEI.
PhylomeDBiO50008.

Enzyme and pathway databases

UniPathwayiUPA00051; UER00082.
BioCyciARA:AT5G17920-MONOMER.
ARA:GQT-1534-MONOMER.
BRENDAi2.1.1.14. 399.
SABIO-RKO50008.

Miscellaneous databases

EvolutionaryTraceiO50008.
PROiO50008.

Gene expression databases

GenevisibleiO50008. AT.

Family and domain databases

HAMAPiMF_00172. Meth_synth.
InterProiIPR013215. Cbl-indep_Met_Synth_N.
IPR006276. Cobalamin-indep_Met_synthase.
IPR002629. Met_Synth_C/arc.
[Graphical view]
PfamiPF08267. Meth_synt_1. 1 hit.
PF01717. Meth_synt_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000382. MeTrfase_B12_ind. 1 hit.
TIGRFAMsiTIGR01371. met_syn_B12ind. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The specific features of methionine biosynthesis and metabolism in plants."
    Ravanel S., Gakiere B., Job D., Douce R.
    Proc. Natl. Acad. Sci. U.S.A. 95:7805-7812(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], CHARACTERIZATION.
    Strain: cv. Columbia.
  2. "Characterization of the cDNA and gene for a cytosolic cobalamin-independent methionine synthase in Arabidopsis thaliana."
    Gakiere B., Job D., Douce R., Ravanel S.
    Plant Gene Register PGR99-115
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  3. "Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol."
    Ravanel S., Block M.A., Rippert P., Jabrin S., Curien G., Rebeille F., Douce R.
    J. Biol. Chem. 279:22548-22557(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    Strain: cv. Wassilewskija.
  4. "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones."
    Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N., Tabata S.
    DNA Res. 5:131-145(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  5. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  6. "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.
  7. "Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis."
    Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.
    Plant J. 59:344-358(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-406.
  8. "Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate."
    Ferrer J.L., Ravanel S., Robert M., Dumas R.
    J. Biol. Chem. 279:44235-44238(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH 5-METHYLTETRAHYDROFOLATE; METHIONINE AND ZINC IONS.

Entry informationi

Entry nameiMETE1_ARATH
AccessioniPrimary (citable) accession number: O50008
Secondary accession number(s): Q6KCR2, Q8H162, Q93ZK3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: June 1, 1998
Last modified: February 17, 2016
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.