ID H5TCE4_9ALTE Unreviewed; 1244 AA.
AC H5TCE4;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 27-MAR-2024, entry version 66.
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:GAB55971.1};
GN ORFNames=GPUN_1855 {ECO:0000313|EMBL:GAB55971.1};
OS Glaciecola punicea ACAM 611.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales;
OC Alteromonadaceae; Glaciecola.
OX NCBI_TaxID=1121923 {ECO:0000313|EMBL:GAB55971.1, ECO:0000313|Proteomes:UP000053586};
RN [1] {ECO:0000313|EMBL:GAB55971.1, ECO:0000313|Proteomes:UP000053586}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ACAM 611 {ECO:0000313|EMBL:GAB55971.1,
RC ECO:0000313|Proteomes:UP000053586};
RX PubMed=22628500; DOI=10.1128/JB.00463-12;
RA Qin Q.-L., Xie B.-B., Shu Y.-L., Rong J.-C., Zhao D.-L., Zhang X.-Y.,
RA Chen X.-L., Zhou B.-C., Zhanga Y.-Z.;
RT "Genome sequence of proteorhodopsin-containing sea ice bacterium Glaciecola
RT punicea ACAM 611T.";
RL J. Bacteriol. 194:3267-3267(2012).
RN [2] {ECO:0000313|EMBL:GAB55971.1, ECO:0000313|Proteomes:UP000053586}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ACAM 611 {ECO:0000313|EMBL:GAB55971.1,
RC ECO:0000313|Proteomes:UP000053586};
RX PubMed=25009843;
RA Qin Q.-L., Xie B.-B., Yu Y., Shu Y.-L., Rong J.-C., Zhang Y.-J.,
RA Zhao D.-L., Chen X.-L., Zhang X.-Y., Chen B., Zhou B.-C., Zhang Y.-Z.;
RT "Comparative genomics of the marine bacterial genus Glaciecola reveals the
RT high degree of genomic diversity and genomic characteristic for cold
RT adaptation.";
RL Environ. Microbiol. 16:1642-1653(2014).
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}.
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:GAB55971.1}.
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DR EMBL; BAET01000019; GAB55971.1; -; Genomic_DNA.
DR RefSeq; WP_006005610.1; NZ_BAET01000019.1.
DR AlphaFoldDB; H5TCE4; -.
DR STRING; 56804.BAE46_06700; -.
DR eggNOG; COG0646; Bacteria.
DR eggNOG; COG1410; Bacteria.
DR OrthoDB; 9803687at2; -.
DR UniPathway; UPA00051; UER00081.
DR Proteomes; UP000053586; Unassembled WGS sequence.
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:UP000053586};
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 9..329
FT /note="Hcy-binding"
FT /evidence="ECO:0000259|PROSITE:PS50970"
FT DOMAIN 360..621
FT /note="Pterin-binding"
FT /evidence="ECO:0000259|PROSITE:PS50972"
FT DOMAIN 653..747
FT /note="B12-binding N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51337"
FT DOMAIN 749..884
FT /note="B12-binding"
FT /evidence="ECO:0000259|PROSITE:PS51332"
FT DOMAIN 899..1231
FT /note="AdoMet activation"
FT /evidence="ECO:0000259|PROSITE:PS50974"
FT BINDING 251
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 314
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 315
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 697
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 759..763
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 762
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 807
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 811
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 863
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 949
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 1138
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 1193..1194
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ SEQUENCE 1244 AA; 137176 MW; 8B272528BA328E78 CRC64;
MAKPQQFPSS LLEQQLAKRI LLLDGAMGTM IQAYDFSEED YRGERFANWS CDVKGNNDLL
VLSQPHIIST IHREYLAAGA DILETNTFNA TRIAMADYEM ENLSREINVQ AAKIARKVAD
EYTALNPDKP RFVAGVLGPT NRTCSISPDV NDPAFRNVTF DELKDAYIES ILALLEGGAD
IIMIETIFDT LNAKAAVFAV EQVFSDLGKR YPVMISGTIT DASGRTLSGQ TTEAFYNSLA
HAKPISFGLN CALGPKELRQ YVEELSRISS CAVSAHPNAG LPNAFGGYDL DAQEMNEHIK
EWAQSGLLNI VGGCCGTTPE HIRVMAEVLA NIPPRIIKDI KVACRLSGLE ALTIDAKSLF
VNVGERTNVT GSALFKKLIV EELYDDALSV ALQQVENGAQ IIDINMDEGM LDSKTAMQRF
LNMIAGEPDI AKVPIMIDSS KWDILEAGLK CVQGKGIVNS ISLKEGEDNF REQAELIRRY
GAAVIVMAFD EVGQADTRVR KFQICQRAYN ILVDELNFPP QDIIFDPNIF AVATGIEEHN
NYAVDFIEAV ADIKKNLPHA MISGGVSNVS FSFRGNNAVR EAIHAVFLYY AIKNGMDMGI
VNAGQLAILK DVPADLRKAV EHVVQNSDDG ATERLLDVAA KYSSTGGAKS SVLDLSWREL
STHKRLEHAL VKGINAFIIE DTEAARLEAK IPLHVIEGPL MDGMNIVGDL FGEGQMFLPQ
VVKSARVMKQ AVAHLQPFIE EGKTEITDNG KVLMATVKGD VHDIGKNIVG VVLQCNNFAI
TDLGVMVACE KILTTARELK VDVIGLSGLI TPSLDEMVHI AKEMQRQGFT IPLLIGGATT
SKAHTAVKIQ PHYKHGVVYV PNASRSVSVV QTLLNSGKAE FLANIDKEYE KVRARHYAKG
PRSTLVSLEK ARANAVPLSF DKYVPVKPQK LGVTVLNDVP LDIVREYIDW TPFFMTWQLS
GKYPRILEHE LIGEVATDLF NDANKMLDEI IGNKSICGKA VFGLFPANRV GDDIEVYLDE
SRTKVNKKLC QLRQQSKKPT GQFNRCLSDY IAHKNDGIED YIGAFAVSAG FGGDALVAQY
DKENDTYNSI LCKAVTDRLA EALAEYLHQQ IRMVYWGYTK DEKLDNTALI RESYQGIRPA
PGYPACPEHT EKGVLWELLD VENNIGMTLT SSFAMWPGAA VSGWYFAHPE SKYFAVAKLT
QDQVHDYAKR KNMHVKEAER WLAANLDYEP EQAETVVQAE LAVV
//
