METE2_ORYSJ
ID METE2_ORYSJ Reviewed; 766 AA.
AC Q2QLY4; A0A0P0YCT2;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 2;
DE EC=2.1.1.14;
DE AltName: Full=Cobalamin-independent methionine synthase 2;
GN OrderedLocusNames=Os12g0624000, LOC_Os12g42884; ORFNames=OsJ_36927;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Ilpoombyeo; TISSUE=Immature seed;
RA Yoon U.H.;
RT "Structural and expression analysis of immature seed genes in Oryza sativa
RT L.";
RL Submitted (OCT-2011) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Catalyzes the transfer of a methyl group from 5-
CC methyltetrahydrofolate to homocysteine resulting in methionine
CC formation. {ECO:0000250}.
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 -!- 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: Cytoplasm, cytosol {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the vitamin-B12 independent methionine synthase
CC family. {ECO:0000305}.
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DR EMBL; JN944357; AFI71268.1; -; mRNA.
DR EMBL; DP000011; ABA99428.1; -; Genomic_DNA.
DR EMBL; DP000011; ABA99429.1; -; Genomic_DNA.
DR EMBL; AP008218; BAF30333.1; -; Genomic_DNA.
DR EMBL; AP014968; BAT18164.1; -; Genomic_DNA.
DR EMBL; CM000149; EEE53643.1; -; Genomic_DNA.
DR EMBL; AK067726; BAG90565.1; -; mRNA.
DR RefSeq; XP_015619851.1; XM_015764365.1.
DR AlphaFoldDB; Q2QLY4; -.
DR SMR; Q2QLY4; -.
DR BioGRID; 821870; 1.
DR STRING; 4530.OS12T0624000-02; -.
DR PaxDb; Q2QLY4; -.
DR PRIDE; Q2QLY4; -.
DR EnsemblPlants; Os12t0624000-01; Os12t0624000-01; Os12g0624000.
DR EnsemblPlants; Os12t0624000-02; Os12t0624000-02; Os12g0624000.
DR GeneID; 4352833; -.
DR Gramene; Os12t0624000-01; Os12t0624000-01; Os12g0624000.
DR Gramene; Os12t0624000-02; Os12t0624000-02; Os12g0624000.
DR KEGG; osa:4352833; -.
DR eggNOG; KOG2263; Eukaryota.
DR HOGENOM; CLU_013175_0_0_1; -.
DR InParanoid; Q2QLY4; -.
DR OMA; KVMKGML; -.
DR OrthoDB; 237390at2759; -.
DR UniPathway; UPA00051; UER00082.
DR Proteomes; UP000000763; Chromosome 12.
DR Proteomes; UP000007752; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 12.
DR Genevisible; Q2QLY4; OS.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0003871; F:5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009086; P:methionine biosynthetic process; IEA:UniProtKB-KW.
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 2: Evidence at transcript level;
KW Amino-acid biosynthesis; Cytoplasm; Metal-binding; Methionine biosynthesis;
KW Methyltransferase; Reference proteome; Transferase; Zinc.
FT CHAIN 1..766
FT /note="5-methyltetrahydropteroyltriglutamate--homocysteine
FT methyltransferase 2"
FT /id="PRO_0000424359"
FT ACT_SITE 702
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 18
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 116
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 438..440
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 438..440
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 491
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 491
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 496
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 519
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 522..523
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 568
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 606
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 606
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000250|UniProtKB:P82610"
FT BINDING 648
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 650
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 659
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O50008"
FT BINDING 672
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 734
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O50008"
SQ SEQUENCE 766 AA; 84666 MW; D594F4DF2708A8B4 CRC64;
MASHIVGYPR MGPKRELKFA LESFWDGKSS AEDLEKVATD LRASIWKQMA DAGIKYIPSN
TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG FSTYFSMARG NATVPAMEMT KWFDTNYHFI
VPELGPNTKF SYSSHKAVNE YKEAKALGVD TVPVLVGPVS YLLLSKPAKG VEKSFALLSL
LSSILPVYKE VIAELKAAGA TWIQFDEPTL VLDLDSHQLA AFSAAYTELE SALSGLNVLI
ETYFADIPAE SYKTLTSLNS VTAYGFDLIR GSKTLDLVKS AGFPSGKYLF AGVVDGRNIW
ADDLAASLTT LESLEAIVGK DKLVVSTSCS LMHTAVDLVN ETKLDSEIKS WLAFAAQKVV
EVNALAKALA GQKDEAYFAA NTAAQASRRS SPRVTNEEVQ KAAAALRGSD HRRATNVSAR
LDAQQKKLNL PVLPTTTIGS FPQTVELRRV RREYKAKKIS EDEYVSAIKE EISKVVKIQE
ELDIDVLVHG EPERNDMVEY FGEQLSGFAF TANGWVQSYG SRCVKPPIIY GDVSRPNAMT
VFWSKMAQSM TSRPMKGMLT GPVTILNWSF VRNDQPRFET CYQIALAIKK EVEDLEAGGI
QVIQIDEAAL REGLPLRKAE HAFYLDWAVH SFRITNCGVQ DTTQIHTHMC YSNFNDIIHS
IINMDADVIT IENSRSDEKL LSVFREGVKY GAGIGPGVYD IHSPRIPSTE EIADRINKML
AVLDTNILWV NPDCGLKTRK YTEVKPALTN MVLAAKLIRT QLASAK
