METE3_ARATH
ID METE3_ARATH Reviewed; 812 AA.
AC Q0WNZ5; Q6KCR0;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic;
DE EC=2.1.1.14;
DE AltName: Full=Cobalamin-independent methionine synthase 3;
DE Short=AtMS3;
DE Flags: Precursor;
GN Name=MS3; OrderedLocusNames=At5g20980; ORFNames=F22D1;
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], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Wassilewskija;
RX PubMed=15024005; DOI=10.1074/jbc.m313250200;
RA Ravanel S., Block M.A., Rippert P., Jabrin S., Curien G., Rebeille F.,
RA Douce R.;
RT "Methionine metabolism in plants: chloroplasts are autonomous for de novo
RT methionine synthesis and can import S-adenosylmethionine from the
RT cytosol.";
RL J. Biol. Chem. 279:22548-22557(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
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;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the transfer of a methyl group from 5-
CC methyltetrahydrofolate to homocysteine resulting in methionine
CC formation. {ECO:0000269|PubMed:15024005}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-
CC methionine + tetrahydropteroyltri-L-glutamate; Xref=Rhea:RHEA:21196,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:58140, ChEBI:CHEBI:58199,
CC ChEBI:CHEBI:58207; EC=2.1.1.14;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17 uM for 5-methyltetrahydrofolate {ECO:0000269|PubMed:15024005};
CC Vmax=0.6 nmol/min/mg enzyme toward 5-methyltetrahydrofolate
CC {ECO:0000269|PubMed:15024005};
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC pathway; L-methionine from L-homocysteine (MetE route): step 1/1.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:15024005}.
CC -!- TISSUE SPECIFICITY: Expressed in seeds. {ECO:0000269|PubMed:15024005}.
CC -!- SIMILARITY: Belongs to the vitamin-B12 independent methionine synthase
CC family. {ECO:0000305}.
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DR EMBL; AJ608675; CAE55865.1; -; mRNA.
DR EMBL; AF296834; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED92915.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92916.1; -; Genomic_DNA.
DR EMBL; AK229291; BAF01154.1; -; mRNA.
DR RefSeq; NP_001078611.1; NM_001085142.1.
DR RefSeq; NP_197598.2; NM_122107.4.
DR AlphaFoldDB; Q0WNZ5; -.
DR SMR; Q0WNZ5; -.
DR IntAct; Q0WNZ5; 1.
DR MINT; Q0WNZ5; -.
DR STRING; 3702.AT5G20980.2; -.
DR iPTMnet; Q0WNZ5; -.
DR PaxDb; Q0WNZ5; -.
DR PRIDE; Q0WNZ5; -.
DR ProteomicsDB; 232295; -.
DR EnsemblPlants; AT5G20980.1; AT5G20980.1; AT5G20980.
DR EnsemblPlants; AT5G20980.2; AT5G20980.2; AT5G20980.
DR GeneID; 832223; -.
DR Gramene; AT5G20980.1; AT5G20980.1; AT5G20980.
DR Gramene; AT5G20980.2; AT5G20980.2; AT5G20980.
DR KEGG; ath:AT5G20980; -.
DR Araport; AT5G20980; -.
DR TAIR; locus:2147147; AT5G20980.
DR eggNOG; KOG2263; Eukaryota.
DR HOGENOM; CLU_013175_0_0_1; -.
DR InParanoid; Q0WNZ5; -.
DR OMA; GWKNGEI; -.
DR OrthoDB; 237390at2759; -.
DR PhylomeDB; Q0WNZ5; -.
DR BioCyc; ARA:AT5G20980-MON; -.
DR SABIO-RK; Q0WNZ5; -.
DR UniPathway; UPA00051; UER00082.
DR PRO; PR:Q0WNZ5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q0WNZ5; baseline and differential.
DR Genevisible; Q0WNZ5; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0003871; F:5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008705; F:methionine synthase activity; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009086; P:methionine biosynthetic process; IMP:TAIR.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR CDD; cd03311; CIMS_C_terminal_like; 1.
DR Gene3D; 3.20.20.210; -; 2.
DR HAMAP; MF_00172; Meth_synth; 1.
DR InterPro; IPR013215; Cbl-indep_Met_Synth_N.
DR InterPro; IPR006276; Cobalamin-indep_Met_synthase.
DR InterPro; IPR002629; Met_Synth_C/arc.
DR InterPro; IPR038071; UROD/MetE-like_sf.
DR Pfam; PF08267; Meth_synt_1; 1.
DR Pfam; PF01717; Meth_synt_2; 1.
DR PIRSF; PIRSF000382; MeTrfase_B12_ind; 1.
DR SUPFAM; SSF51726; SSF51726; 2.
DR TIGRFAMs; TIGR01371; met_syn_B12ind; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; Chloroplast; Metal-binding;
KW Methionine biosynthesis; Methyltransferase; Plastid; Reference proteome;
KW Transferase; Transit peptide; Zinc.
FT TRANSIT 1..33
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 34..812
FT /note="5-methyltetrahydropteroyltriglutamate--homocysteine
FT methyltransferase 3, chloroplastic"
FT /id="PRO_0000424357"
FT REGION 13..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 430..456
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 16..30
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 430..445
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 749
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 66
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 164
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 485..487
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 485..487
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 538
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 538
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 543
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 566
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 569..570
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 615
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 653
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 653
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 695
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 697
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 706
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 710
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 719
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 781
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT CONFLICT 11
FT /note="P -> L (in Ref. 1; CAE55865)"
FT /evidence="ECO:0000305"
FT CONFLICT 77
FT /note="T -> S (in Ref. 1; CAE55865)"
FT /evidence="ECO:0000305"
FT CONFLICT 634
FT /note="A -> G (in Ref. 1; CAE55865)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 812 AA; 90594 MW; 976DC8AC06A1DF27 CRC64;
MGQLALQRLQ PLASLPRRPP SLPPPSSATP SLPCATASRR PRFYVARAMS SHIVGYPRIG
PKRELKFALE SFWDGKTNVD DLQNVAANLR KSIWKHMAHA GIKYIPSNTF SYYDQMLDTT
AMLGAVPSRY GWESGEIGFD VYFSMARGNA SAHAMEMTKW FDTNYHYIVP ELGPDVNFSY
ASHKAVVEFK EAKALGIDTV PVLIGPMTYL LLSKPAKGVE KSFCLLSLID KILPVYKEVL
ADLKSAGARW IQFDEPILVM DLDTSQLQAF SDAYSHMESS LAGLNVLIAT YFADVPAEAY
KTLMSLKCVT GFGFDLVRGL ETLDLIKMNF PRGKLLFAGV VDGRNIWAND LSASLKTLQT
LEDIVGKEKV VVSTSCSLLH TAVDLVNEMK LDKELKSWLA FAAQKVVEVN ALAKSFSGAK
DEALFSSNSM RQASRRSSPR VTNAAVQQDV DAVKKSDHHR STEVSVRLQA QQKKLNLPAL
PTTTIGSFPQ TTDLRRIRRE FKAKKISEVD YVQTIKEEYE KVIKLQEELG IDVLVHGEAE
RNDMVEFFGE QLSGFAFTSN GWVQSYGSRC VKPPIIYGDI TRPKAMTVFW SSMAQKMTQR
PMKGMLTGPV TILNWSFVRN DQPRHETCFQ IALAIKDEVE DLEKAGVTVI QIDEAALREG
LPLRKSEQKF YLDWAVHAFR ITNSGVQDST QIHTHMCYSN FNDIIHSIID MDADVITIEN
SRSDEKLLSV FHEGVKYGAG IGPGVYDIHS PRIPSTEEIA ERINKMLAVL DSKVLWVNPD
CGLKTRNYSE VKSALSNMVA AAKLIRSQLN KS
