ID A0A2N3IKX8_9BACT Unreviewed; 1414 AA.
AC A0A2N3IKX8;
DT 25-APR-2018, integrated into UniProtKB/TrEMBL.
DT 25-APR-2018, sequence version 1.
DT 27-MAR-2024, entry version 27.
DE RecName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998};
DE EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032};
DE AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00031040};
GN ORFNames=Rain11_0059 {ECO:0000313|EMBL:PKQ70918.1};
OS Raineya orbicola.
OC Bacteria; Bacteroidota; Cytophagia; Cytophagales; Raineyaceae; Raineya.
OX NCBI_TaxID=2016530 {ECO:0000313|EMBL:PKQ70918.1, ECO:0000313|Proteomes:UP000233387};
RN [1] {ECO:0000313|EMBL:PKQ70918.1, ECO:0000313|Proteomes:UP000233387}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SPSPC-11 {ECO:0000313|EMBL:PKQ70918.1,
RC ECO:0000313|Proteomes:UP000233387};
RA Albuquerque L., Polonia A.R.M., Barroso C., Froufe H.J.C., Lage O.,
RA Lobo-Da-Cunha A., Egas C., Da Costa M.S.;
RT "Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of
RT the phylum Bacteroidetes and the description of Raineyaceae fam. nov.";
RL Submitted (JUN-2017) 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 -!- 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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|ARBA:ARBA00001947,
CC 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|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}.
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:PKQ70918.1}.
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DR EMBL; NKXO01000001; PKQ70918.1; -; Genomic_DNA.
DR UniPathway; UPA00051; UER00081.
DR Proteomes; UP000233387; Unassembled WGS sequence.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0008705; F:methionine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0042558; P:pteridine-containing compound metabolic process; IEA:InterPro.
DR CDD; cd01038; Endonuclease_DUF559; 1.
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; 2.
DR Gene3D; 3.40.960.10; VSR Endonuclease; 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; IPR007569; DUF559.
DR InterPro; IPR047216; Endonuclease_DUF559_bact.
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; IPR011335; Restrct_endonuc-II-like.
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; PF04480; DUF559; 1.
DR Pfam; PF02965; Met_synt_B12; 2.
DR Pfam; PF00809; Pterin_bind; 1.
DR Pfam; PF02574; S-methyl_trans; 1.
DR PIRSF; PIRSF000381; MetH; 2.
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; 2.
DR SUPFAM; SSF47644; Methionine synthase domain; 1.
DR SUPFAM; SSF52980; Restriction endonuclease-like; 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 Cobalamin {ECO:0000256|ARBA:ARBA00022628, ECO:0000256|PIRSR:PIRSR000381-1};
KW Cobalt {ECO:0000256|ARBA:ARBA00023285};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRSR:PIRSR000381-1};
KW Methionine biosynthesis {ECO:0000256|ARBA:ARBA00023167};
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|PROSITE-
KW ProRule:PRU00346}; Reference proteome {ECO:0000313|Proteomes:UP000233387};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691,
KW ECO:0000256|PIRSR:PIRSR000381-2};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|PROSITE-
KW ProRule:PRU00346};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|PIRSR:PIRSR000381-1}.
FT DOMAIN 3..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 898..1414
FT /note="AdoMet activation"
FT /evidence="ECO:0000259|PROSITE:PS50974"
FT BINDING 245
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 948
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 1324
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
FT BINDING 1379..1380
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PIRSR:PIRSR000381-2"
SQ SEQUENCE 1414 AA; 159164 MW; 9A723DC1AAD89987 CRC64;
MTSPNIYDIL KERILVLDGA MGTMIQQYKL TEADYRGERF KDFPHDLKGN NDLLSITQPH
IIQEIHRKYL EAGADIIETN TFNGTRISMA DYHMEDLVYE LNFQSAKIAK EVCEEFTRQN
PAKPRFVAGS IGPTNKTASL SPDVNNPGYR AITFDELVEA YTEQIRGLID GGADILLIET
IFDTLNAKAA LFAIETYFEK TGKRLPIMVS GTITDASGRT LSGQTAEAFL ISVSHLPLLS
VGFNCALGAD LLRPYSEEIA KKAPFYTSAH PNAGLPNAFG EYDQSPEEMA KIVEDFLKDG
LVNIIGGCCG TTPAHIKLIA ELAQKYKPRP LPQDDEISKY SGLEPLKATK EIRFINVGER
TNVTGSRAFA RLIKEEKYEE ALAVARTQVE GGAQMIDVNM DEGMLDSEKA MVTFLNLIAS
EPDIARLPIM IDSSKWSVIE AGLKCVQGKA VVNSISLKEG EEDFIKKAKL IKKYGAAVIV
MAFDEQGQAD TYERRIQICE RAYKILTEKV GFPPEDIIFD PNILTVATGI EEHNNYAVDF
VRATEWIKKN LPYAKVSGGV SNISFSFRGN DVVREAMHSA FLYRAIQAGM DMGIVNAGQL
AVYEEIPKDL LELVEDVLWN RRPDATERLV AFAEQIKNKS GKTQEIDLAW RNEPVEKRLA
HALIKGIADF IETDVEEARQ KYAHPLQIIE GPLMDGMNIV GDLFGEGKMF LPQVVKSARV
MKKAVAYLLP FMEAEKKENQ NSMGAGKILL ATVKGDVHDI GKNIVGVVLA CNGFEIIDLG
VMVPTQKILE EARKHQVDII GLSGLITPSL DEMVSVAKEM EREGFKIPLL IGGATTSKAH
TAVKIAPNYS EPVIHVLDAS RSVPVATKLL SKQKGEKENF VAEIKQEYDK IRNDFLNRKQ
EKNYISLQEA RKNKFKIDWA KTQIHKPKFL GNKYFINYDL AEIAKYIDWT PFFQTWELAG
KFPQILDDEI VGTEARKLYE DAQKMLAEII QNKSLQANAV IGFYPCNTIN DDDILLYDFE
ETEVITPCTK HNGHAHKKYE VLKKPLLLKN SHPLIFENRL TGGISNIKEL ETKRKALRNG
ATKAEKFLWK FLQKSQLGRK FRRQHSVENF ILDFYCPEEK LAIELDGKGH FSPVGQEYDL
YRDTRLAELG LKVLHFENKL VLENIESVLA EIKNNYGWYK NQPPLTPPWK GVEKASPLLS
EEGKGVVYNP HWAIIHTLRQ QNQKSEGLPN FALADFIAPQ ETEQVDYMGF FAVTAGIGLE
KLVEKYEKDH DDYNSIMAKA LADRLAEAFA ELMHERVRKE FWGYSPDENF TNEELIKEKY
VGIRPAPGYP ACPDHTEKAT IFELLQATEK IGLQLTESFA MYPAAAVCGM YFAHPESRYF
GLGKISKDQV VEYAERKQMS VEEVEKWLSS ILNY
//
