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Database: UniProt
Entry: I2BDY8_SHIBC
LinkDB: I2BDY8_SHIBC
Original site: I2BDY8_SHIBC 
ID   I2BDY8_SHIBC            Unreviewed;      1227 AA.
AC   I2BDY8; K6W2L6;
DT   11-JUL-2012, integrated into UniProtKB/TrEMBL.
DT   11-JUL-2012, sequence version 1.
DT   27-MAR-2024, entry version 83.
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   Name=metH {ECO:0000313|EMBL:AFJ48742.1};
GN   OrderedLocusNames=EBL_c36910 {ECO:0000313|EMBL:AFJ48742.1};
OS   Shimwellia blattae (strain ATCC 29907 / DSM 4481 / JCM 1650 / NBRC 105725 /
OS   CDC 9005-74) (Escherichia blattae).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Shimwellia.
OX   NCBI_TaxID=630626 {ECO:0000313|EMBL:AFJ48742.1, ECO:0000313|Proteomes:UP000001955};
RN   [1] {ECO:0000313|EMBL:AFJ48742.1, ECO:0000313|Proteomes:UP000001955}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 29907 / DSM 4481 / JCM 1650 / NBRC 105725 / CDC 9005-74
RC   {ECO:0000313|Proteomes:UP000001955};
RX   PubMed=22843577; DOI=10.1128/JB.00829-12;
RA   Brzuszkiewicz E., Waschkowitz T., Wiezer A., Daniel R.;
RT   "Complete genome sequence of the B12-producing Shimwellia blattae strain
RT   DSM 4481, isolated from a cockroach.";
RL   J. Bacteriol. 194:4436-4436(2012).
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; CP001560; AFJ48742.1; -; Genomic_DNA.
DR   RefSeq; WP_002445425.1; NZ_BAHA01000046.1.
DR   AlphaFoldDB; I2BDY8; -.
DR   SMR; I2BDY8; -.
DR   STRING; 630626.EBL_c36910; -.
DR   KEGG; ebt:EBL_c36910; -.
DR   PATRIC; fig|630626.3.peg.3609; -.
DR   eggNOG; COG0646; Bacteria.
DR   eggNOG; COG1410; Bacteria.
DR   HOGENOM; CLU_004914_2_2_6; -.
DR   OrthoDB; 9803687at2; -.
DR   UniPathway; UPA00051; UER00081.
DR   Proteomes; UP000001955; 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_sf.
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};
KW   Reference proteome {ECO:0000313|Proteomes:UP000001955};
KW   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          650..744
FT                   /note="B12-binding N-terminal"
FT                   /evidence="ECO:0000259|PROSITE:PS51337"
FT   DOMAIN          746..881
FT                   /note="B12-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS51332"
FT   DOMAIN          897..1227
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         694
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         756..760
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         759
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         804
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         808
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         860
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         946
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         1134
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         1189..1190
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ   SEQUENCE   1227 AA;  135985 MW;  BFD9265AC6928E74 CRC64;
     MSNKTEKLHQ QLAQRILVLD GGMGTMIQGY RLDERAFRGE RFADWPCDLK GNNDLLVLTQ
     PEIITAIHNA YFEAGADIIE TNTFNSTTIA MADYQMESLS AEINYAAARL ARECADAWSA
     REPEKPRYVA GVLGPTNRTA SISPDVNDPA YRNITFDQLV AAYRESTRAL VEGGVDLILI
     ETVFDTLNAK AAIFAVETEF EALGQSLPVM ISGTITDASG RTLSGQTTEA FYNSLRHAGA
     LSFGLNCALG PDELRQYVAE MSRIAECYVS AHPNAGLPNA FGEYDLDADT MAAQVKEWAE
     SGFLNIVGGC CGTTPAHIAA MSRAVAGVAP RKRPVLPVAC RLSGLEPLNI GEDSLFVNVG
     ERTNVTGSAK FKRLIKEEKY SEALDVARQQ VENGAQIIDI NMDEGMLDAE AAMVRFLNLI
     AGEPDIARVP IMIDSSKWEV IEKGLKCIQG KGIVNSISMK EGVEAFTEHA KRVRRYGAAM
     VVMAFDEQGQ ADTRERKREI CTRAYNILTR EVGFPPEDII FDPNIFAVAT GIEEHNNYAV
     DFIGACEDIK RDLPHALISG GVSNVSFSFR GNDPVREAIH AVFLYYAIRN GMDMGIVNAG
     QLAIYDDLPG ELRDAVEDVI LNRRDDGTER LLALAEKYRG SKTDEAANTQ LAEWRNWEVK
     KRLEYSLVKG ITEFIEQDTE EARQQADRPI EVIEGPLMDG MNVVGDLFGE GKMFLPQVVK
     SARVMKQAVA YLEPFIEASK EKGQSNGKMV IATVKGDVHD IGKNIVGVVL QCNNYEIIDL
     GVMVPAEKIL KTAREENADL IGLSGLITPS LDEMVHVAKE MERQGFTIPL LIGGATTSKA
     HTAVKIEQNY SGPTVYVQNA SRTVGVVSSL LSATQRDDFI ARTRKEYETV RTQHGRKKPR
     TPPVTLQAAR ENDFAFDWES YTPPVAHRLG VQEVTASIET LRNYIDWTPF FMTWTLAGKY
     PRILEDEVVG EEAQRLFADA NAMLDMLSET KALNPRGVVG LFPANRVGDD VEIYQDETRT
     RVLAVGHHLR QQTEKVGYAN YCLADFVAPR HTRKADYIGA FAVTGGLEED ALADAYEARH
     DDYNKIMVKS VADRLAEAFA EYLHERVRKV YWGYAPTENL SNEALIRENY QGIRPAPGYP
     ACPEHTEKET IWKLLDVEAR IGMKLTESCA MWPGASVSGW YFSHPESKYF AVAQIQRDQV
     EDYARRKGMS LAEAERWLAP NLGYDAD
//
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