ID D7DQ65_METV0 Unreviewed; 762 AA.
AC D7DQ65;
DT 10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT 10-AUG-2010, sequence version 1.
DT 24-JAN-2024, entry version 72.
DE RecName: Full=5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase {ECO:0000256|HAMAP-Rule:MF_00172};
DE EC=2.1.1.14 {ECO:0000256|HAMAP-Rule:MF_00172};
DE AltName: Full=Cobalamin-independent methionine synthase {ECO:0000256|HAMAP-Rule:MF_00172};
DE AltName: Full=Methionine synthase, vitamin-B12 independent isozyme {ECO:0000256|HAMAP-Rule:MF_00172};
GN Name=metE {ECO:0000256|HAMAP-Rule:MF_00172};
GN OrderedLocusNames=M301_1052 {ECO:0000313|EMBL:ADI29436.1};
OS Methylotenera versatilis (strain 301).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales;
OC Methylophilaceae; Methylotenera.
OX NCBI_TaxID=666681 {ECO:0000313|EMBL:ADI29436.1, ECO:0000313|Proteomes:UP000000383};
RN [1] {ECO:0000313|Proteomes:UP000000383}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 {ECO:0000313|Proteomes:UP000000383};
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Clum A., Land M., Hauser L., Kyrpides N., Ivanova N.,
RA Chistoservova L., Kalyuzhnaya M., Woyke T.;
RT "Complete sequence of Methylotenera sp. 301.";
RL Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ADI29436.1, ECO:0000313|Proteomes:UP000000383}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 {ECO:0000313|EMBL:ADI29436.1,
RC ECO:0000313|Proteomes:UP000000383};
RX PubMed=21622745; DOI=10.1128/JB.00404-11;
RA Lapidus A., Clum A., Labutti K., Kaluzhnaya M.G., Lim S., Beck D.A.,
RA Glavina Del Rio T., Nolan M., Mavromatis K., Huntemann M., Lucas S.,
RA Lidstrom M.E., Ivanova N., Chistoserdova L.;
RT "Genomes of three methylotrophs from a single niche uncover genetic and
RT metabolic divergence of Methylophilaceae.";
RL J. Bacteriol. 193:3757-3764(2011).
CC -!- FUNCTION: Catalyzes the transfer of a methyl group from 5-
CC methyltetrahydrofolate to homocysteine resulting in methionine
CC formation. {ECO:0000256|ARBA:ARBA00002777, ECO:0000256|HAMAP-
CC Rule:MF_00172}.
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; Evidence={ECO:0000256|HAMAP-
CC Rule:MF_00172};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00172};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00172};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|PIRSR:PIRSR000382-2};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000256|PIRSR:PIRSR000382-
CC 2};
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC pathway; L-methionine from L-homocysteine (MetE route): step 1/1.
CC {ECO:0000256|ARBA:ARBA00004681, ECO:0000256|HAMAP-Rule:MF_00172}.
CC -!- SIMILARITY: Belongs to the vitamin-B12 independent methionine synthase
CC family. {ECO:0000256|ARBA:ARBA00009553, ECO:0000256|HAMAP-
CC Rule:MF_00172}.
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DR EMBL; CP002056; ADI29436.1; -; Genomic_DNA.
DR RefSeq; WP_013147752.1; NC_014207.1.
DR AlphaFoldDB; D7DQ65; -.
DR STRING; 666681.M301_1052; -.
DR KEGG; meh:M301_1052; -.
DR eggNOG; COG0620; Bacteria.
DR HOGENOM; CLU_013175_0_0_4; -.
DR OrthoDB; 244285at2; -.
DR UniPathway; UPA00051; UER00082.
DR Proteomes; UP000000383; Chromosome.
DR GO; GO:0003871; F:5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009086; P:methionine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR CDD; cd03311; CIMS_C_terminal_like; 1.
DR CDD; cd03312; CIMS_N_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 NCBIfam; TIGR01371; met_syn_B12ind; 1.
DR PANTHER; PTHR30519; 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE; 1.
DR PANTHER; PTHR30519:SF0; 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE; 1.
DR Pfam; PF08267; Meth_synt_1; 1.
DR Pfam; PF01717; Meth_synt_2; 1.
DR PIRSF; PIRSF000382; MeTrfase_B12_ind; 1.
DR SUPFAM; SSF51726; UROD/MetE-like; 2.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Methionine biosynthesis {ECO:0000256|ARBA:ARBA00023167, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP-
KW Rule:MF_00172}; Reference proteome {ECO:0000313|Proteomes:UP000000383};
KW Repeat {ECO:0000256|HAMAP-Rule:MF_00172};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_00172}.
FT DOMAIN 8..312
FT /note="Cobalamin-independent methionine synthase MetE N-
FT terminal"
FT /evidence="ECO:0000259|Pfam:PF08267"
FT DOMAIN 433..755
FT /note="Cobalamin-independent methionine synthase MetE C-
FT terminal/archaeal"
FT /evidence="ECO:0000259|Pfam:PF01717"
FT ACT_SITE 701
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-3"
FT BINDING 20..23
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 23
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 120
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 125
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 438..440
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 438..440
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 491
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 491
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 522..523
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 568
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 606
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 606
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 612
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 648
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 648
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 650
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 650
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 672
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 672
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 733
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 733
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
SQ SEQUENCE 762 AA; 85628 MW; 1FCEEC4ECDA88F5D CRC64;
MTKNNIKAHI LGYPRVGAKR ELKFALESFW RKEVSSDDLQ NTAKNLRAEH WQKQQEAGLA
FITSNDFSLY DHVLDHSVLF GAQPKRFNKK PFGEANPAPE NAYFALARGN LEQPAMEMTK
WFDTNYHYIV PELASDTQFS INVHDFLSQL DEAQKISKNV KPVLLGPVSF LYLSKARGIN
KLDLLDGLAQ QYVYLLQELQ LRKIEWLQVD EPIFALDLDD AWLKAFDHAY SWFRTSRPKL
LLTTYFANVS RYQAFITNLP VDGIHIDLVR APEQLGPWVN AIPSHWVISA GVIDGRNIWR
NDLDKTLALL DPWVKRLGDR LWIAPSCSLL HTPVTLAHEV KLDAEIKSWL AFADEKIIEL
SIIAKALNNG VDSVAQELAI SRAAIASRNQ SNRVHDANVK ARIAALNTLN ENRESTFELR
AKAQKARLNL PLLPTTTIGS FPQTPDIRAA RAAYKKGDIS QAKYDAEMEA HIAYAIAQQE
EIGLDVLVHG EAERNDMVEF FGEQLAGYAF TQNGWVQSYG SRCVKPPVIY GDVHRPKAMT
VGTASFAQSL SSRPVKGMLT GPITILQWSF VRDDQPRETT AMQLALAIRD EVEDLQKAGI
AIIQIDEPAL REGLPLQKAA WAQYLAWAVK AFKLSASIAR DDTQIHTHMC YAEFNDILPA
IAAMDADVIT IETSRSAMEL LDAFGEFSYP NDIGPGVYDI HSPRVPSVEA MEKLMKRAFD
VVPIERLWIN PDCGLKTRGW PETKTALENM VTVAKSLREQ LA
//
