ID A0A2Z6EY78_9BURK Unreviewed; 928 AA.
AC A0A2Z6EY78;
DT 10-OCT-2018, integrated into UniProtKB/TrEMBL.
DT 10-OCT-2018, sequence version 1.
DT 27-MAR-2024, entry version 21.
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 Name=metH1 {ECO:0000313|EMBL:GLR00784.1};
GN ORFNames=GCM10007934_05950 {ECO:0000313|EMBL:GLR00784.1}, MCB1EB_2206
GN {ECO:0000313|EMBL:BBE10367.1};
OS Mycoavidus cysteinexigens.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Mycoavidus.
OX NCBI_TaxID=1553431 {ECO:0000313|EMBL:BBE10367.1, ECO:0000313|Proteomes:UP000282597};
RN [1] {ECO:0000313|EMBL:BBE10367.1, ECO:0000313|Proteomes:UP000282597}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=B1-EB {ECO:0000313|EMBL:BBE10367.1,
RC ECO:0000313|Proteomes:UP000282597};
RX PubMed=29540638; DOI=10.1264/jsme2.ME17138;
RA Sharmin D., Guo Y., Nishizawa T., Ohshima S., Sato Y., Takashima Y.,
RA Narisawa K., Ohta H.;
RT "Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial
RT Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.";
RL Microbes Environ. 33:66-76(2018).
RN [2] {ECO:0000313|EMBL:GLR00784.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=NBRC 110909 {ECO:0000313|EMBL:GLR00784.1};
RX PubMed=30832757;
RA Wu L., Ma J.;
RT "The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing
RT project: providing services to taxonomists for standard genome sequencing
RT and annotation.";
RL Int. J. Syst. Evol. Microbiol. 69:895-898(2019).
RN [3] {ECO:0000313|EMBL:GLR00784.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=NBRC 110909 {ECO:0000313|EMBL:GLR00784.1};
RA Sun Q., Mori K.;
RT "Draft genome sequence of Mycoavidus cysteinexigens strain NBRC 110909.";
RL Submitted (JAN-2023) 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|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; AP018150; BBE10367.1; -; Genomic_DNA.
DR EMBL; BSOD01000005; GLR00784.1; -; Genomic_DNA.
DR RefSeq; WP_045364183.1; NZ_BSOD01000005.1.
DR AlphaFoldDB; A0A2Z6EY78; -.
DR GeneID; 84624808; -.
DR KEGG; mcys:MCB1EB_2206; -.
DR UniPathway; UPA00051; UER00081.
DR Proteomes; UP000282597; Chromosome.
DR Proteomes; UP001156688; 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; 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; 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:UP000282597};
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 37..298
FT /note="Pterin-binding"
FT /evidence="ECO:0000259|PROSITE:PS50972"
FT DOMAIN 335..429
FT /note="B12-binding N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51337"
FT DOMAIN 438..577
FT /note="B12-binding"
FT /evidence="ECO:0000259|PROSITE:PS51332"
FT DOMAIN 592..928
FT /note="AdoMet activation"
FT /evidence="ECO:0000259|PROSITE:PS50974"
FT BINDING 379
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 448..452
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 451
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 496
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 500
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 556
FT /ligand="methylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:28115"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 642
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 841
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 895..896
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ SEQUENCE 928 AA; 102510 MW; 2006E8B753104742 CRC64;
MTDATDLNRR APHQIGLEPA LRLAGLEAFN IGAQTRFVNI GERTNVTGSK AFARMILNDE
FDAALSVARQ QVENGAQIID INMDEAMLDS KAAMVRFLNL IAAEPDIARV PIMLDSSKWE
VLEAGLKCVQ GKAIVNSISL KEGVEIFKQQ AQSIRRYGAA AVVMAFDETG QADSFARKIT
ICERSYRILV EEVGFAPEDI IFDPNIFAIA TGIDEHNNYA VDFIEATRWI KAHLPYAKVS
GGVSNVSFSF RGNDAVREAI HTVFLYHAIS AGMDMGIVNA GQLGIYAELD PTLRERVEDV
VLNRSVQTAN GMSATERLLE ITEHFKQGGG AKNQEALLWR QLSVKDRLAH ALVHGITEFI
IEDTEEARQQ YARPIQVIEG PLMDGMNRVG DLFGAGKMFL PQVVKSARVM KQAVAHLLPF
IEAEKNLLTA QGGDAKPKGK MVIATVKGDV HDIGKNIVSV VLQCNNFEVI NMGVMVPCSE
ILAKAKAENA DMIGLSGLIT PSLEEMAYVA AEIQRDEILR ARNIPLLIGG ATTSRVHTAV
KIAPQYGGPV IYVPDASRAV SVASSLLSET HSATYIAELK TNYERIREQH ANKKTQPMVS
LSQARANRHR INWTTTSPTK PKLIGRRVLK NYDLAELARY IDWGPFFQTW DLAGPFPAIL
TDAIVGEAAR RVYEDAQNML AQLIAGRWLT AHGVFALLPA NTVNDDDIEI YTDETRKQIA
LTWHTLRQQS ERPVIEGPNQ EKIRRPNRAL ADFIAPKETQ IDDYIGLFAV TAGLNIDKKV
QQFEQAQDDY SAIMLKALAD RLAESFAERL HERIRTEFWG YAAAEQLSHN ELINEKYVGI
RPAPGYPACP DHLVKQAMFS LMHCDEIDMQ LTESLAMLPA ASVSGFYLAH PDSTYFSVGK
IGTDQLDDYA RRTGLSITDA QRALAASL
//
