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Database: UniProt
Entry: A1VIG4_POLNA
LinkDB: A1VIG4_POLNA
Original site: A1VIG4_POLNA 
ID   A1VIG4_POLNA            Unreviewed;       939 AA.
AC   A1VIG4;
DT   06-FEB-2007, integrated into UniProtKB/TrEMBL.
DT   06-FEB-2007, sequence version 1.
DT   24-JAN-2024, entry version 106.
DE   RecName: Full=Methionine synthase {ECO:0000256|PIRNR:PIRNR000381};
DE            EC=2.1.1.13 {ECO:0000256|PIRNR:PIRNR000381};
DE   AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|PIRNR:PIRNR000381};
GN   OrderedLocusNames=Pnap_0117 {ECO:0000313|EMBL:ABM35442.1};
OS   Polaromonas naphthalenivorans (strain CJ2).
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Polaromonas.
OX   NCBI_TaxID=365044 {ECO:0000313|EMBL:ABM35442.1, ECO:0000313|Proteomes:UP000000644};
RN   [1] {ECO:0000313|Proteomes:UP000000644}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CJ2 {ECO:0000313|Proteomes:UP000000644};
RX   PubMed=19453698; DOI=10.1111/j.1462-2920.2009.01947.x;
RA   Yagi J.M., Sims D., Brettin T., Bruce D., Madsen E.L.;
RT   "The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal
RT   tar-contaminated sediment, reveals physiological and metabolic versatility
RT   and evolution through extensive horizontal gene transfer.";
RL   Environ. Microbiol. 11:2253-2270(2009).
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|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|PIRNR:PIRNR000381};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000256|PIRNR:PIRNR000381};
CC   -!- COFACTOR:
CC       Name=methylcob(III)alamin; Xref=ChEBI:CHEBI:28115;
CC         Evidence={ECO:0000256|PIRNR:PIRNR000381,
CC         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|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; CP000529; ABM35442.1; -; Genomic_DNA.
DR   AlphaFoldDB; A1VIG4; -.
DR   STRING; 365044.Pnap_0117; -.
DR   KEGG; pna:Pnap_0117; -.
DR   eggNOG; COG1410; Bacteria.
DR   HOGENOM; CLU_004914_2_0_4; -.
DR   OMA; ADCIAMS; -.
DR   UniPathway; UPA00051; UER00081.
DR   Proteomes; UP000000644; 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; 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; 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   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; 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; PS50972; PTERIN_BINDING; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis {ECO:0000256|PIRNR:PIRNR000381};
KW   Cobalamin {ECO:0000256|PIRNR:PIRNR000381, ECO:0000256|PIRSR:PIRSR000381-1};
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|PIRNR:PIRNR000381};
KW   Methyltransferase {ECO:0000256|ARBA:ARBA00022603,
KW   ECO:0000256|PIRNR:PIRNR000381};
KW   Reference proteome {ECO:0000313|Proteomes:UP000000644};
KW   Repeat {ECO:0000256|ARBA:ARBA00022737};
KW   S-adenosyl-L-methionine {ECO:0000256|PIRNR:PIRNR000381,
KW   ECO:0000256|PIRSR:PIRSR000381-2};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|PIRNR:PIRNR000381};
KW   Zinc {ECO:0000256|PIRNR:PIRNR000381}.
FT   DOMAIN          29..290
FT                   /note="Pterin-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS50972"
FT   DOMAIN          329..427
FT                   /note="B12-binding N-terminal"
FT                   /evidence="ECO:0000259|PROSITE:PS51337"
FT   DOMAIN          436..575
FT                   /note="B12-binding"
FT                   /evidence="ECO:0000259|PROSITE:PS51332"
FT   DOMAIN          589..939
FT                   /note="AdoMet activation"
FT                   /evidence="ECO:0000259|PROSITE:PS50974"
FT   BINDING         377
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         446..450
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         449
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         494
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         498
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         554
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         639
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         852
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT   BINDING         906..907
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ   SEQUENCE   939 AA;  103069 MW;  FCC32E3A91CE6F7F CRC64;
     MSSIQFSHEV PPMKLSGLEP VTIGSDSLFV NIGERTNVTG SKAFARMILN GDYEQALTVA
     RQQVENGAQI IDINMDEAML DSQAAMVRFL NLIAGEPDIA RVPIMIDSSK WSVIEAGLRC
     IQGKGIVNSI SMKEGVDAFK HQAKLLKRYG AAAVVMAFDE KGQADTYERK ISICERAYRV
     LVDEIGFPPE DIIFDPNIFA IATGIDEHNN YAVDFIEATR WIKANLPGAK VSGGVSNVSF
     SFRGNDPVRE AIHTVFLYHA IQAGMDMGIV NAGMMGVYDE LEPVLRERVE DVVLNRQPVY
     KPGEAHLTPG ERLIEVAETA KSGARDDSKK YEWRALPIRA RLSHALVHGN NEFITEDTEE
     VWQAIKAEGG RPLHVIEGPL MDGMNVVGDL FGQGKMFLPQ VVKSARVMKQ AVAHLLPYIE
     AEKLLLEAAG GDVKTKGKII IATVKGDVHD IGKNIVTVVL QCNNFEVVNM GVMVPCHEIL
     ALAKAEGAHI VGLSGLITPS LEEMQYVAAE MQKDDHFRLN KIPLMIGGAT TSRVHTAVKI
     SPHYEGPVVY VPDASRSVSV AQSLLSEQAA KYIAELNADY DKVRTQHANK KQTPMWPLAK
     ARANATPIDW TNYTPPVPKF IGRRVFKNFD LAELAQFIDW GPFFQTWDLA GPFPAILTDE
     VVGVEATRVY EDAQKMLKRL IEGRWLTASG VMALLPANSV GDDIEIYTDE TRTEVAMTWH
     GLRQQTEKTA VDGVMRPSRC LADFVAPKVL TPELIAARTR AASAKGQNDL KIADYIGVFA
     VTAGLGADKK EKAFQADHDD YSSIMFKSLA DRLAEAFAEA LHQRVRRDLW GYAPAESLGH
     DALIAEQYQG IRPAPGYPAC PDHSVKKEMF ELLHAGDIGM ALTESLAMTP AASVSGFYLS
     HPQSTYFSVG KIGDDQLQDL ARRRGAKAED LARLLAPNL
//
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