ID A0A402CYI3_9BACT Unreviewed; 1227 AA.
AC A0A402CYI3;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 27-MAR-2024, entry version 19.
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:BDI31354.1};
GN ORFNames=CCAX7_34050 {ECO:0000313|EMBL:BDI31354.1}, CCAX7_35030
GN {ECO:0000313|EMBL:GCE54989.1};
OS Capsulimonas corticalis.
OC Bacteria; Armatimonadota; Armatimonadia; Capsulimonadales;
OC Capsulimonadaceae; Capsulimonas.
OX NCBI_TaxID=2219043 {ECO:0000313|EMBL:GCE54989.1};
RN [1] {ECO:0000313|EMBL:GCE54989.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX-7 {ECO:0000313|EMBL:GCE54989.1};
RA Li J., Tonouchi A.;
RT "Draft Genome Sequence of Capsulimonas corticalis strain AX-7.";
RL Int. J. Syst. Evol. Microbiol. 0:0-0(2018).
RN [2] {ECO:0000313|EMBL:BDI31354.1, ECO:0000313|Proteomes:UP000287394}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX-7 {ECO:0000313|EMBL:BDI31354.1,
RC ECO:0000313|Proteomes:UP000287394};
RA Li J., Kudo C., Tonouchi A.;
RT "Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated
RT bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the
RT class Armatimonadia of the phylum Armatimonadetes.";
RL Int. J. Syst. Evol. Microbiol. 69:220-226(2019).
RN [3] {ECO:0000313|EMBL:BDI31354.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AX-7 {ECO:0000313|EMBL:BDI31354.1};
RA Li J., Tonouchi A.;
RL Submitted (MAY-2022) to the EMBL/GenBank/DDBJ databases.
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; AP025739; BDI31354.1; -; Genomic_DNA.
DR EMBL; BHFQ01000008; GCE54989.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A402CYI3; -.
DR KEGG; ccot:CCAX7_34050; -.
DR InParanoid; A0A402CYI3; -.
DR OrthoDB; 9803687at2; -.
DR UniPathway; UPA00051; UER00081.
DR Proteomes; UP000287394; 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:UP000287394};
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 1..323
FT /note="Hcy-binding"
FT /evidence="ECO:0000259|PROSITE:PS50970"
FT DOMAIN 354..615
FT /note="Pterin-binding"
FT /evidence="ECO:0000259|PROSITE:PS50972"
FT DOMAIN 646..740
FT /note="B12-binding N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51337"
FT DOMAIN 745..880
FT /note="B12-binding"
FT /evidence="ECO:0000259|PROSITE:PS51332"
FT DOMAIN 896..1227
FT /note="AdoMet activation"
FT /evidence="ECO:0000259|PROSITE:PS50974"
FT BINDING 243
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 308
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 309
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 690
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 755..759
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 758
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 803
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 807
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 859
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; 134906 MW; 9A00B3C233A06E9F CRC64;
MADIREELKK RILVIDGAMG TMIQRYKPTE ADYRGERFAN HPVDLKNNNE ALMLVRPEII
EEIHMAYLDA GADIIETNTF NANSISMADF EMADLVREMN FEAVAVARRA IDKAMAADPS
KPRFIAGALG PCTRSATVIE DSNNPAYRSF TFDDFEATYY EQAKALLDAG TDLLLCETTF
DTLNLKAALF AIQRLFDEGE RVVPVMASLS ITDLGGGNLT GQNLEAMWNS IAHAPLLSVG
LNCGFGPDVY RPFVEEISRI APIFVSIYPN AGLPNALAET GFDLDEPQMT PSIREWAENG
WLNIIGGCCG TTPEFIRGFA KAVEGLPPRV PPVIAPEMRL SGTQAFNVGE DTLFVNVGER
TNVTGSPKFA KLILAGDYEA ALTVAQQQVD NGAQVIDVNM DEGLLDSEKA MTTFLTLIQG
ETNINKVPIM VDSSKWSVIE AGLKALPGKG IVNSISLKEG EEKFKEQAKL VKRYGAAVVV
MAFDEVGQAD SEDRKVEICT RAYNILTQEV GFLPQDIIFD PNILTIATGI EEHNNYAVDF
INATRRIKET LPLAKVSGGV SNLSFSFRGN NVVREAIHSA FLYHAIKAGL DMGIVNAGML
EVYEAIPKDL LGLVEDALFN RRPDSTERLL EFAEGLKGVK GKVVVKDEAW RNETVESRLS
YALVKGVTEY IEADTEEARL KYDKPLEVIE GPLMAGMNVV GDLFGSGKMF LPQVVKSARV
MKRAVAVLMP YMEAEKLASG NTQAQAKVLM ATVKGDVHDI GKNIVGVVLG CNNYDVIDMG
VMVPSDKILA AAIEQEVDII GLSGLITPSL DEMIHVAKEM QRQGFTKPLL IGGATTSRTH
TAVKIAQAYE GPIVHVLDAS RAVGVVSNLI SDDLRPDFVE KNRAEQAATR VTFANKRSQK
DTLPFEAAKA NRTPIVWSPE DIAKPEFTGV RVLKDFPLSE LVPYIDWGPF FIAWELHGKY
PAIFEDEIVG ERAKELFEDG QEILKKLLQD GQLKASGVYG FFPANSVGED IELYTDDTRT
EVLTTIHALR QQTPKTSGES NKSLSDYIAP RETGLADYLG AFAVTTGLGI EPIVAQYERD
LDDYNAIMVK ALADRLAEAF AEYLHAQARR DWGFGVSENL TNEDLIRERY RGIRPAPGYP
ACPDHTESKT MFELLLVEEN TGITLTESMA KYPTASVNGW YLAHPEAKYF GVGKIGKDQV
EDYAGRKGWD LKTAEYWLSP NLNYDPE
//
