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METH_VIBVU
ID   METH_VIBVU              Reviewed;        1226 AA.
AC   Q8DCJ7;
DT   22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   03-AUG-2022, entry version 120.
DE   RecName: Full=Methionine synthase;
DE            EC=2.1.1.13;
DE   AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase;
DE   AltName: Full=Methionine synthase, vitamin-B12 dependent;
DE            Short=MS;
GN   Name=metH; OrderedLocusNames=VV1_1423;
OS   Vibrio vulnificus (strain CMCP6).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=216895;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CMCP6;
RA   Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E.;
RT   "Complete genome sequence of Vibrio vulnificus CMCP6.";
RL   Submitted (DEC-2002) 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 (By similarity). {ECO:0000250}.
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   -!- COFACTOR:
CC       Name=methylcob(III)alamin; Xref=ChEBI:CHEBI:28115;
CC         Evidence={ECO:0000250};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000250};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC       pathway; L-methionine from L-homocysteine (MetH route): step 1/1.
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 (By similarity). {ECO:0000250}.
CC   -!- MISCELLANEOUS: L-homocysteine is bound via the zinc atom.
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the vitamin-B12 dependent methionine synthase
CC       family. {ECO:0000305}.
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DR   EMBL; AE016795; AAO09863.1; -; Genomic_DNA.
DR   RefSeq; WP_011079382.1; NC_004459.3.
DR   AlphaFoldDB; Q8DCJ7; -.
DR   SMR; Q8DCJ7; -.
DR   PRIDE; Q8DCJ7; -.
DR   EnsemblBacteria; AAO09863; AAO09863; VV1_1423.
DR   KEGG; vvu:VV1_1423; -.
DR   HOGENOM; CLU_004914_2_2_6; -.
DR   OMA; ADCIAMS; -.
DR   UniPathway; UPA00051; UER00081.
DR   Proteomes; UP000002275; Chromosome 1.
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; cd02069; methionine_synthase_B12_BD; 1.
DR   Gene3D; 1.10.1240.10; -; 1.
DR   Gene3D; 3.10.196.10; -; 1.
DR   Gene3D; 3.20.20.20; -; 1.
DR   Gene3D; 3.20.20.330; -; 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; 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   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; SSF47644; SSF47644; 1.
DR   SUPFAM; SSF51717; SSF51717; 1.
DR   SUPFAM; SSF52242; SSF52242; 1.
DR   SUPFAM; SSF56507; SSF56507; 1.
DR   SUPFAM; SSF82282; SSF82282; 1.
DR   TIGRFAMs; TIGR02082; metH; 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; Cobalamin; Cobalt; Metal-binding;
KW   Methionine biosynthesis; Methyltransferase; Repeat;
KW   S-adenosyl-L-methionine; Transferase; Zinc.
FT   CHAIN           1..1226
FT                   /note="Methionine synthase"
FT                   /id="PRO_0000204542"
FT   DOMAIN          6..326
FT                   /note="Hcy-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00333"
FT   DOMAIN          357..618
FT                   /note="Pterin-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00334"
FT   DOMAIN          651..745
FT                   /note="B12-binding N-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00667"
FT   DOMAIN          747..882
FT                   /note="B12-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00666"
FT   DOMAIN          898..1226
FT                   /note="AdoMet activation"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00346"
FT   BINDING         248
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00333"
FT   BINDING         311
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00333"
FT   BINDING         312
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00333"
FT   BINDING         695
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000250|UniProtKB:P13009"
FT   BINDING         757..761
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000250|UniProtKB:P13009"
FT   BINDING         760
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:0000250|UniProtKB:P13009"
FT   BINDING         805
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000250|UniProtKB:P13009"
FT   BINDING         809
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000250|UniProtKB:P13009"
FT   BINDING         861
FT                   /ligand="methylcob(III)alamin"
FT                   /ligand_id="ChEBI:CHEBI:28115"
FT                   /evidence="ECO:0000250|UniProtKB:P13009"
FT   BINDING         948
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         1136
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         1191..1192
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1226 AA;  136241 MW;  51E8263EBD605A19 CRC64;
     MGSQIRAQIE AQLKQRILLI DGGMGTMIQG YKLQEQDYRG ERFADWHSDL KGNNDLLVLT
     QPQLIKEIHH AYLEAGADIL ETNTFNATTI AMADYDMESL SEEINFAAAR LAREAADEWT
     AQNPAKPRYV AGVLGPTNRT CSISPDVNDP GYRNVSFDEL VEAYSESTRA LIRGGSDLIL
     IETIFDTLNA KACAFAVDSV FEELGFALPV MISGTITDAS GRTLSGQTTE AFYNSLRHVR
     PISFGLNCAL GPDELRPYVE ELSRISETFV STHPNAGLPN AFGEYDLSPE EMAEHVKEWA
     QSGFLNLIGG CCGTTPEHIR HMAMAVEGVS PRVLPEIPVA CRLSGLEPLT IAKDTLFVNV
     GERTNVTGSA RFKRLIKEEL YDEALDVARE QVENGAQIID INMDEGMLDA EACMVRFLNL
     CASEPEISKV PIMVDSSKWE VIEAGLKCIQ GKGIVNSISL KEGKEKFVEQ AKLIRRYGAA
     VIVMAFDEVG QADTRERKLE ICTKAYRILV DEVGFPPEDV IFDPNIFAVA TGIDEHNNYA
     VDFIEAVADI KRDLPHAMIS GGVSNVSFSF RGNNYVREAI HAVFLYHCFK NGMDMGIVNA
     GQLEIYDNVP EKLREAVEDV VLNRRDDATE RLLEIAEEYR ENAVGKQEDA SALEWRTWSV
     EKRLEHALVK GITEFIVEDT EEARLNASKP LEVIEGPLMD GMNVVGDLFG EGKMFLPQVV
     KSARVMKQAV AHLEPFINAS KQAGSSNGKI LLATVKGDVH DIGKNIVGVV LQCNNYEIID
     LGVMVPCEQI LKVAKEQQVD IIGLSGLITP SLDEMVHVAK EMERLGFDLP LLIGGATTSK
     AHTAVKIEQN YSHPVVYVNN ASRAVGVCTS LLSDELRPAF VERLQADYEL VRDQHNRKKP
     RTKPVTLEAA RANKVAIDWQ SYTPPAPSQP GVHVFDDFDV ATLRQYIDWT PFFLTWSLVG
     KYPTIFEHEE VGEEAKRLFG DANEWLDRIE QEGLLKARGM CGLFPAASVG DDIEVYTDES
     RTHVAKVLHN LRQQTEKPKG ANYCLSDYVA PKESGKKDWI GAFAVTGGVN ERELADQFKA
     QGDDYNAIMI QAVADRLAEA FAEYLHERVR KEIWGYAADE NLSNEELIRE KYQGIRPAPG
     YPACPEHTEK GPLWELLNVE ETIGMSLTSS YAMWPGASVS GWYFSHPDSR YFAIAQIQQD
     QVESYAERKG WDLLEAEKWL GPNING
 
 
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