ID A0A023D815_ACIMT Unreviewed; 754 AA.
AC A0A023D815;
DT 11-JUN-2014, integrated into UniProtKB/TrEMBL.
DT 11-JUN-2014, sequence version 1.
DT 24-JAN-2024, entry version 45.
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 ORFNames=Amme_114_015 {ECO:0000313|EMBL:GAJ30258.1};
OS Acidomonas methanolica NBRC 104435.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales;
OC Acetobacteraceae; Acidomonas.
OX NCBI_TaxID=1231351 {ECO:0000313|EMBL:GAJ30258.1, ECO:0000313|Proteomes:UP000019760};
RN [1] {ECO:0000313|Proteomes:UP000019760}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MB58 {ECO:0000313|Proteomes:UP000019760};
RX PubMed=24330138; DOI=10.1111/1574-6968.12357;
RA Higashiura N., Hadano H., Hirakawa H., Matsutani M., Takabe S.,
RA Matsushita K., Azuma Y.;
RT "Draft Genomic DNA Sequence of the Facultatively Methylotrophic Bacterium
RT Acidomonas methanolica type strain MB58.";
RL FEMS Microbiol. Lett. 351:9-13(2014).
RN [2] {ECO:0000313|EMBL:GAJ30258.1, ECO:0000313|Proteomes:UP000019760}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MB58 {ECO:0000313|EMBL:GAJ30258.1,
RC ECO:0000313|Proteomes:UP000019760};
RA Higashiura N., Hadano H., Hirakawa H., Matsutani M., Takabe S.,
RA Matsushita K., Azuma Y.;
RT "Draft genomic DNA sequence of the facultatively methylotrophic bacterium
RT Acidomonas methanolica type strain MB58.";
RL FEMS Microbiol. Lett. 351:9-13(2014).
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}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00172}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:GAJ30258.1}.
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DR EMBL; BAND01000113; GAJ30258.1; -; Genomic_DNA.
DR RefSeq; WP_042061100.1; NZ_BJVB01000015.1.
DR AlphaFoldDB; A0A023D815; -.
DR OrthoDB; 244285at2; -.
DR UniPathway; UPA00051; UER00082.
DR Proteomes; UP000019760; Unassembled WGS sequence.
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:UP000019760};
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 6..311
FT /note="Cobalamin-independent methionine synthase MetE N-
FT terminal"
FT /evidence="ECO:0000259|Pfam:PF08267"
FT DOMAIN 428..750
FT /note="Cobalamin-independent methionine synthase MetE C-
FT terminal/archaeal"
FT /evidence="ECO:0000259|Pfam:PF01717"
FT REGION 395..415
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 395..414
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 696
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-3"
FT BINDING 17..20
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 20
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 113
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 118
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 433..435
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 433..435
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 486
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 486
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 563
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 601
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 601
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 607
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 643
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 643
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 645
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 645
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 667
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 667
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 728
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 728
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 754 AA; 82923 MW; AA952FD2A5F11B62 CRC64;
MGVSVATLGF PRIGPRRELK TALESYWSGK APRQTLLDTA AALRAENWKR QQEGGADIVP
SNDFSLYDHV LDNSALFGVV PEAYGWDGGT VGLDTYFAMA RGAAGVTAGE MTKWFDTNYH
YLVPEFSAGQ AFRLASTKIV DEFLEAKAQG LVTRPVLLGP VTYLLLGKAR DGADPLTLLP
KLLPAYAEVL GRLADAGAEW VQIDEPALVL DLTAEARAAF GAAYTHLTRA APSLKLMLAT
YFGALGDNLA TALALPVQGL HVDLARAPEQ LAAVVAGARP DLLLSLGVID GRNIWRADLS
ALLDRLEPVV KARGNVVIAP SCSLIHVPID LARETDLDPD VASWLAFAVQ KIEELRILAL
ALNEGRDAAT EALAASDRAR DARRISPKIH DPAVRDRLAT QGEHDSRRAS PFGTRREAQR
AALGLPAWPT TTIGSFPQTP EVRRARADHA KGALSDESYT AFLREETARA VRWQEEVGLD
ALVHGEFERN DMVQYFGEQL AGFVFTKHGW VQSYGSRYVR PPIIFGDVSR PAAMTVEWWR
YAQSLTERPL KGMLTGPVTI LNWSFVRDDQ PRSVTCRQIA FAIRDEVLDL EKAGARMIQI
DEAALREGLP LRRAEWRNYL DWAVESFRIA ASGVADATQI HTHMCYSEFN DIIAAIGAMD
ADVISIETAR SRMELLDAFA EYAYPAEIGP GVYDIHSPRV PDVEEMVALL RAARKRLDDD
QIWVNPDCGL KTRKWEEVRP AIVNMVSAAR MLRG
//
