ID C5CR21_VARPS Unreviewed; 781 AA.
AC C5CR21;
DT 28-JUL-2009, integrated into UniProtKB/TrEMBL.
DT 28-JUL-2009, sequence version 1.
DT 27-MAR-2024, entry version 79.
DE RecName: Full=5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase {ECO:0000256|HAMAP-Rule:MF_00172};
DE EC=2.1.1.14 {ECO:0000256|HAMAP-Rule:MF_00172};
DE AltName: Full=Cobalamin-independent methionine synthase {ECO:0000256|HAMAP-Rule:MF_00172};
DE AltName: Full=Methionine synthase, vitamin-B12 independent isozyme {ECO:0000256|HAMAP-Rule:MF_00172};
GN Name=metE {ECO:0000256|HAMAP-Rule:MF_00172};
GN OrderedLocusNames=Vapar_3248 {ECO:0000313|EMBL:ACS19866.1};
OS Variovorax paradoxus (strain S110).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Variovorax.
OX NCBI_TaxID=543728 {ECO:0000313|EMBL:ACS19866.1};
RN [1] {ECO:0000313|EMBL:ACS19866.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=S110 {ECO:0000313|EMBL:ACS19866.1};
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D.,
RA Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Ovchinnikova G., Orwin P.,
RA Leadbetter J.R., Spain J.C., Han J.I.;
RT "Complete sequence of chromosome 1 of Variovorax paradoxus S110.";
RL Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the transfer of a methyl group from 5-
CC methyltetrahydrofolate to homocysteine resulting in methionine
CC formation. {ECO:0000256|ARBA:ARBA00002777, ECO:0000256|HAMAP-
CC Rule:MF_00172}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-
CC methionine + tetrahydropteroyltri-L-glutamate; Xref=Rhea:RHEA:21196,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:58140, ChEBI:CHEBI:58199,
CC ChEBI:CHEBI:58207; EC=2.1.1.14; Evidence={ECO:0000256|HAMAP-
CC Rule:MF_00172};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00172};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00172};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|PIRSR:PIRSR000382-2};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000256|PIRSR:PIRSR000382-
CC 2};
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC pathway; L-methionine from L-homocysteine (MetE route): step 1/1.
CC {ECO:0000256|ARBA:ARBA00004681, ECO:0000256|HAMAP-Rule:MF_00172}.
CC -!- SIMILARITY: Belongs to the vitamin-B12 independent methionine synthase
CC family. {ECO:0000256|ARBA:ARBA00009553, ECO:0000256|HAMAP-
CC Rule:MF_00172}.
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DR EMBL; CP001635; ACS19866.1; -; Genomic_DNA.
DR AlphaFoldDB; C5CR21; -.
DR STRING; 543728.Vapar_3248; -.
DR KEGG; vap:Vapar_3248; -.
DR eggNOG; COG0620; Bacteria.
DR HOGENOM; CLU_013175_0_0_4; -.
DR OrthoDB; 244285at2; -.
DR UniPathway; UPA00051; UER00082.
DR GO; GO:0003871; F:5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009086; P:methionine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR CDD; cd03311; CIMS_C_terminal_like; 1.
DR CDD; cd03312; CIMS_N_terminal_like; 1.
DR Gene3D; 3.20.20.210; -; 2.
DR HAMAP; MF_00172; Meth_synth; 1.
DR InterPro; IPR013215; Cbl-indep_Met_Synth_N.
DR InterPro; IPR006276; Cobalamin-indep_Met_synthase.
DR InterPro; IPR002629; Met_Synth_C/arc.
DR InterPro; IPR038071; UROD/MetE-like_sf.
DR NCBIfam; TIGR01371; met_syn_B12ind; 1.
DR PANTHER; PTHR30519; 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE; 1.
DR PANTHER; PTHR30519:SF0; 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE; 1.
DR Pfam; PF08267; Meth_synt_1; 1.
DR Pfam; PF01717; Meth_synt_2; 1.
DR PIRSF; PIRSF000382; MeTrfase_B12_ind; 1.
DR SUPFAM; SSF51726; UROD/MetE-like; 2.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Methionine biosynthesis {ECO:0000256|ARBA:ARBA00023167, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP-
KW Rule:MF_00172}; Repeat {ECO:0000256|HAMAP-Rule:MF_00172};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00172};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_00172}.
FT DOMAIN 5..326
FT /note="Cobalamin-independent methionine synthase MetE N-
FT terminal"
FT /evidence="ECO:0000259|Pfam:PF08267"
FT DOMAIN 444..772
FT /note="Cobalamin-independent methionine synthase MetE C-
FT terminal/archaeal"
FT /evidence="ECO:0000259|Pfam:PF01717"
FT ACT_SITE 718
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-3"
FT BINDING 17..20
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 20
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 129
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 134
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 449..451
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 449..451
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 502
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 502
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 533..534
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 579
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 617
FT /ligand="L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:58199"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 617
FT /ligand="L-methionine"
FT /ligand_id="ChEBI:CHEBI:57844"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172,
FT ECO:0000256|PIRSR:PIRSR000382-1"
FT BINDING 623
FT /ligand="5-methyltetrahydropteroyltri-L-glutamate"
FT /ligand_id="ChEBI:CHEBI:58207"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 659
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 659
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 661
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 661
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 683
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 683
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
FT BINDING 750
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|PIRSR:PIRSR000382-2"
FT BINDING 750
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00172"
SQ SEQUENCE 781 AA; 86481 MW; 7E038CFCAB5630AE CRC64;
MTTRTHILGF PRMGAHRELK FALEKHWRGE IDRAALEEVG GQLRARHWQA QRDAGLDYVT
VGDFACYDHV ANHVQLFGCE PARFGFKGDE PELSRYFKMA RGVEDEAGHA HDAGCKHGAE
GAFALEMTKW FDTNYHYLVP EFTAATQFRL ASTRLFDEVA EAQQAGHAVK AVLLGPLSFL
YLGKEKQQGF DRLSLLDALL PVYEQVLNRL KQQGVEWVQI DEPILGLDLP DAWRNAFERA
YWQLARSASK LLLATYFSPL LGNLRLACQL PVAGLHVDAV RAPQELTGVA DWLATHKVLS
IGIVDGRNIW RTDLDAALAT LRPVIDKRRG ELWIAPSCSL LHVPFSLAAE DKLDAELRSW
LAFAVEKLGE LRVLRAVLDG SEDLVAEELE AARAAVIARR SSPRVHRADV ALRLARSVAG
DDQRASPFGQ RQRLQRARFA LPALPTTTIG SFPQTQEIRA ARAAFKRGEL DAAGYREKMR
AEIALAVRKQ EELGIDVLVH GEAERNDMVE YFGEQLDGFA FTANGWVQSY GSRCVKPPVI
FGDVARPAPM TVEWTAYAQS LTQLPMKGML TGPVTILQWS FVRDDQPRSV TCEQIAWAIR
DEVVDLEAAG IGIIQIDEPA IREGLPLRRA GWPAYLKSAT RAFRISASGV CDQTQVHTHM
CYSEFNDILP EIAAMDADVI TIETSRSDME LLRGFGGENS AGGFRYPNEI GPGVYDIHSP
RVPSVGEIVR LMRKAAGVVP PGNLWINPDC GLKTRGWPET EAALSNMVAA AKLLRAELAA
A
//
