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Entry: D3SCH9_THISK
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ID   D3SCH9_THISK            Unreviewed;      1263 AA.
AC   D3SCH9;
DT   20-APR-2010, integrated into UniProtKB/TrEMBL.
DT   20-APR-2010, sequence version 1.
DT   24-JAN-2024, entry version 94.
DE   RecName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998, ECO:0000256|PIRNR:PIRNR000381};
DE            EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032, ECO:0000256|PIRNR:PIRNR000381};
DE   AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00031040, ECO:0000256|PIRNR:PIRNR000381};
GN   OrderedLocusNames=TK90_0182 {ECO:0000313|EMBL:ADC70698.1};
OS   Thioalkalivibrio sp. (strain K90mix).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales;
OC   Ectothiorhodospiraceae; Thioalkalivibrio.
OX   NCBI_TaxID=396595 {ECO:0000313|EMBL:ADC70698.1, ECO:0000313|Proteomes:UP000009099};
RN   [1] {ECO:0000313|Proteomes:UP000009099}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K90mix {ECO:0000313|Proteomes:UP000009099};
RG   US DOE Joint Genome Institute;
RA   Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA   Pitluck S., Foster B., Sun H., Larimer F., Land M., Hauser L., Kyrpides N.,
RA   Ivanova N., Sorokin D.Y., Muyzer G., Woyke T.;
RT   "Complete sequence of chromosome of Thioalkalivibrio sp. K90mix.";
RL   Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:ADC70698.1, ECO:0000313|Proteomes:UP000009099}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K90mix {ECO:0000313|EMBL:ADC70698.1,
RC   ECO:0000313|Proteomes:UP000009099};
RX   PubMed=22675584; DOI=10.4056/sigs.2315092;
RA   Muyzer G., Sorokin D.Y., Mavromatis K., Lapidus A., Foster B., Sun H.,
RA   Ivanova N., Pati A., D'haeseleer P., Woyke T., Kyrpides N.C.;
RT   "Complete genome sequence of Thioalkalivibrio sp. K90mix.";
RL   Stand. Genomic Sci. 5:341-355(2011).
CC   -!- FUNCTION: Catalyzes the transfer of a methyl group from methyl-
CC       cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and
CC       methionine. Subsequently, remethylates the cofactor using
CC       methyltetrahydrofolate. {ECO:0000256|ARBA:ARBA00025552,
CC       ECO:0000256|PIRNR:PIRNR000381}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine =
CC         (6S)-5,6,7,8-tetrahydrofolate + L-methionine; Xref=Rhea:RHEA:11172,
CC         ChEBI:CHEBI:18608, ChEBI:CHEBI:57453, ChEBI:CHEBI:57844,
CC         ChEBI:CHEBI:58199; EC=2.1.1.13;
CC         Evidence={ECO:0000256|ARBA:ARBA00001700,
CC         ECO:0000256|PIRNR:PIRNR000381};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000256|ARBA:ARBA00001947,
CC         ECO:0000256|PIRNR:PIRNR000381, ECO:0000256|PROSITE-ProRule:PRU00333};
CC   -!- COFACTOR:
CC       Name=methylcob(III)alamin; Xref=ChEBI:CHEBI:28115;
CC         Evidence={ECO:0000256|ARBA:ARBA00001956,
CC         ECO:0000256|PIRNR:PIRNR000381, ECO:0000256|PIRSR:PIRSR000381-1};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC       pathway; L-methionine from L-homocysteine (MetH route): step 1/1.
CC       {ECO:0000256|ARBA:ARBA00005178, ECO:0000256|PIRNR:PIRNR000381}.
CC   -!- DOMAIN: Modular enzyme with four functionally distinct domains. The
CC       isolated Hcy-binding domain catalyzes methyl transfer from free
CC       methylcobalamin to homocysteine. The Hcy-binding domain in association
CC       with the pterin-binding domain catalyzes the methylation of
CC       cob(I)alamin by methyltetrahydrofolate and the methylation of
CC       homocysteine. The B12-binding domain binds the cofactor. The AdoMet
CC       activation domain binds S-adenosyl-L-methionine. Under aerobic
CC       conditions cob(I)alamin can be converted to inactive cob(II)alamin.
CC       Reductive methylation by S-adenosyl-L-methionine and flavodoxin
CC       regenerates methylcobalamin. {ECO:0000256|PIRNR:PIRNR000381}.
CC   -!- SIMILARITY: Belongs to the vitamin-B12 dependent methionine synthase
CC       family. {ECO:0000256|ARBA:ARBA00010398}.
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DR   EMBL; CP001905; ADC70698.1; -; Genomic_DNA.
DR   RefSeq; WP_012981597.1; NC_013889.1.
DR   AlphaFoldDB; D3SCH9; -.
DR   STRING; 396595.TK90_0182; -.
DR   KEGG; tkm:TK90_0182; -.
DR   eggNOG; COG0646; Bacteria.
DR   eggNOG; COG1410; Bacteria.
DR   HOGENOM; CLU_004914_4_0_6; -.
DR   OMA; ADCIAMS; -.
DR   OrthoDB; 9803687at2; -.
DR   UniPathway; UPA00051; UER00081.
DR   Proteomes; UP000009099; Chromosome.
DR   GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0008705; F:methionine synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR   GO; GO:0042558; P:pteridine-containing compound metabolic process; IEA:InterPro.
DR   CDD; cd02069; methionine_synthase_B12_BD; 1.
DR   CDD; cd00740; MeTr; 1.
DR   Gene3D; 3.40.50.280; Cobalamin-binding domain; 1.
DR   Gene3D; 1.10.288.10; Cobalamin-dependent Methionine Synthase, domain 2; 1.
DR   Gene3D; 3.20.20.20; Dihydropteroate synthase-like; 1.
DR   Gene3D; 3.20.20.330; Homocysteine-binding-like domain; 1.
DR   Gene3D; 1.10.1240.10; Methionine synthase domain; 1.
DR   Gene3D; 3.10.196.10; Vitamin B12-dependent methionine synthase, activation domain; 1.
DR   InterPro; IPR003759; Cbl-bd_cap.
DR   InterPro; IPR006158; Cobalamin-bd.
DR   InterPro; IPR036724; Cobalamin-bd_sf.
DR   InterPro; IPR011005; Dihydropteroate_synth-like.
DR   InterPro; IPR003726; HCY_dom.
DR   InterPro; IPR036589; HCY_dom_sf.
DR   InterPro; IPR033706; Met_synthase_B12-bd.
DR   InterPro; IPR011822; MetH.
DR   InterPro; IPR036594; Meth_synthase_dom.
DR   InterPro; IPR000489; Pterin-binding_dom.
DR   InterPro; IPR004223; VitB12-dep_Met_synth_activ_dom.
DR   InterPro; IPR037010; VitB12-dep_Met_synth_activ_sf.
DR   NCBIfam; TIGR02082; metH; 1.
DR   PANTHER; PTHR45833; METHIONINE SYNTHASE; 1.
DR   PANTHER; PTHR45833:SF1; METHIONINE SYNTHASE; 1.
DR   Pfam; PF02310; B12-binding; 1.
DR   Pfam; PF02607; B12-binding_2; 1.
DR   Pfam; PF02965; Met_synt_B12; 1.
DR   Pfam; PF00809; Pterin_bind; 1.
DR   Pfam; PF02574; S-methyl_trans; 1.
DR   PIRSF; PIRSF000381; MetH; 1.
DR   SMART; SM01018; B12-binding_2; 1.
DR   SUPFAM; SSF52242; Cobalamin (vitamin B12)-binding domain; 1.
DR   SUPFAM; SSF51717; Dihydropteroate synthetase-like; 1.
DR   SUPFAM; SSF82282; Homocysteine S-methyltransferase; 1.
DR   SUPFAM; SSF56507; Methionine synthase activation domain-like; 1.
DR   SUPFAM; SSF47644; Methionine synthase domain; 1.
DR   PROSITE; PS50974; ADOMET_ACTIVATION; 1.
DR   PROSITE; PS51332; B12_BINDING; 1.
DR   PROSITE; PS51337; B12_BINDING_NTER; 1.
DR   PROSITE; PS50970; HCY; 1.
DR   PROSITE; PS50972; PTERIN_BINDING; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605,
KW   ECO:0000256|PIRNR:PIRNR000381};
KW   Cobalamin {ECO:0000256|ARBA:ARBA00022628, ECO:0000256|PIRNR:PIRNR000381};
KW   Cobalt {ECO:0000256|ARBA:ARBA00023285, ECO:0000256|PIRNR:PIRNR000381};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW   ECO:0000256|PIRNR:PIRNR000381};
KW   Methionine biosynthesis {ECO:0000256|ARBA:ARBA00023167,
KW   ECO:0000256|PIRNR:PIRNR000381};
KW   Methyltransferase {ECO:0000256|ARBA:ARBA00022603,
KW   ECO:0000256|PIRNR:PIRNR000381}; Repeat {ECO:0000256|ARBA:ARBA00022737};
KW   S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691,
KW   ECO:0000256|PIRNR:PIRNR000381};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|PIRNR:PIRNR000381};
KW   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|PIRNR:PIRNR000381}.
FT   DOMAIN          5..325
FT                   /note="Hcy-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS50970"
FT   DOMAIN          356..617
FT                   /note="Pterin-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS50972"
FT   DOMAIN          648..742
FT                   /note="B12-binding N-terminal"
FT                   /evidence="ECO:0000259|PROSITE:PS51337"
FT   DOMAIN          744..879
FT                   /note="B12-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS51332"
FT   DOMAIN          895..1247
FT                   /note="AdoMet activation"
FT                   /evidence="ECO:0000259|PROSITE:PS50974"
FT   BINDING         247
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-1,
FT                   ECO:0000256|PROSITE-ProRule:PRU00333"
FT   BINDING         310
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-1,
FT                   ECO:0000256|PROSITE-ProRule:PRU00333"
FT   BINDING         311
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-1,
FT                   ECO:0000256|PROSITE-ProRule:PRU00333"
FT   BINDING         692
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         754..758
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         757
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /ligand_part="Co"
FT                   /ligand_part_id="ChEBI:CHEBI:27638"
FT                   /note="axial binding residue"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-1"
FT   BINDING         802
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         806
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         858
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         964
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         1154
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         1209..1210
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ   SEQUENCE   1263 AA;  140733 MW;  43BDBF5409C2DCCE CRC64;
     MTATRNDIEK ALKERILILD GGMGTTIQLY KLEEADYRGE RFKDWESDLK GNNDLLSLTR
     PDIIEQIHND YLEAGADIIE ANTFNGTRIA MADYHMEDLV PELNRESAKL ARKAADAWTE
     KTPDKPRYVA GILGPTNRTA SISPDVNDPG ARNVDFDTLV ESYKEAAEAL VEGGVDILLI
     ETVFDTLNAK AAIFAVKTLE DELGKELPIM ISGTITDASG RTLSGQTTEA FWNSVRHANP
     VSIGLNCALG AKEMRQYVEE LSRIADTHVS AHPNAGLPNE FGDYDESPEQ MAADVGPWAE
     QGLLNIIGGC CGTLPEHIRA MREAVEKFPP RKVPEIAPAC RLSGLEPCNI TDDSLFVNVG
     ERTNVTGSRK FLRLIQNEEY DVALEVALNQ VEGGAQIIDI NMDEGMLESQ DAMVRFLNLL
     AGEPDIARVP VMIDSSKFEI IEAGLKCVQG KAVVNSISMK EGEENFIKQA QLCRRYGAAI
     VVMAFDEDGQ ADNEDRRVEI CTRAYRLLTE KVGFPAEDII FDPNIFAVAT GIEEHNNYGV
     DFIEATRRIK QDLPHALVSG GVSNVSFSFR GNEPVREAIH AVFLYHAIKA GMDMGIVNAG
     QLAVYDDIDE KLKEAVEDVV LNRRDDATER LLDLSEEYKG QGGGKKEENL EWREWEVTKR
     LEHSLVKGID TYVVEDTEEA RQQYDRPIQV IEGPLMDGMN VVGDLFGEGK MFLPQVVKSA
     RVMKKAVAHL IPYIEAEKTG TENNGKILMA TVKGDVHDIG KNIVGVVLQC NNFEVIDIGV
     MQPGAEILKA AKEHDVDVIG LSGLITPSLE EMANFAADLE REGMTTPLMI GGATTSRAHT
     AVKIEPNYSG PVVWVKDASR AVGVAQSLIS PELRENYAAE IREEYEKLRV QNAGRKKKTQ
     WVTLEKARAN KPQIDWSSYT PTKPKALETD KLPGEPKVLH PHGDGSVLLR FDDFDLNEVR
     NFIDWTPFFH SWQLHAAYPR ILDDEKVGEE ARKLFKDGQE MLDRMIEEKW VTLRGVVGFF
     PANTVNDDDI EVYTDESRSK VLKKLHHLRQ QTEKRRGQPS HSLADFLMPK EAGGPDYLGA
     FAVSAGGDVD AKAEEYEKAN DDYHAILVKS LADRLAEAFA ECMHQYVRKH YWGYVPDEAL
     ENEDLIDEKY QGIRPAPGYP ACPEHTEKGT LWELLQADEH ADMTLTESYA MLPVSAVSGW
     YFAHPESRYF GLGKVNRDQV EDYAKRKGMS FEEAERWLAP NIGYDDSDEA KAEARAEREA
     RSA
//
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