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Protein

Probable methionine synthase

Gene

metr-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).By similarity

Catalytic activityi

5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine.

Cofactori

Protein has several cofactor binding sites:

Pathway: L-methionine biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes L-methionine from L-homocysteine (MetH route).
Proteins known to be involved in this subpathway in this organism are:
  1. Probable methionine synthase (metr-1)
This subpathway is part of the pathway L-methionine biosynthesis via de novo pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-methionine from L-homocysteine (MetH route), the pathway L-methionine biosynthesis via de novo pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi249 – 2491ZincPROSITE-ProRule annotation
Metal bindingi312 – 3121ZincPROSITE-ProRule annotation
Metal bindingi313 – 3131ZincPROSITE-ProRule annotation
Metal bindingi775 – 7751Cobalt (cobalamin axial ligand)By similarity
Binding sitei820 – 8201CobalaminBy similarity
Binding sitei963 – 9631S-adenosyl-L-methionineBy similarity
Binding sitei1157 – 11571S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei1161 – 11611Cobalamin; via carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Amino-acid biosynthesis, Methionine biosynthesis

Keywords - Ligandi

Cobalamin, Cobalt, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiREACT_274901. Methylation.
REACT_320610. Sulfur amino acid metabolism.
REACT_347550. Cobalamin (Cbl, vitamin B12) transport and metabolism.
UniPathwayiUPA00051; UER00081.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable methionine synthase (EC:2.1.1.13)
Alternative name(s):
5-methyltetrahydrofolate--homocysteine methyltransferase
Vitamin-B12 dependent methionine synthase
Short name:
MS
Gene namesi
Name:metr-1
ORF Names:R03D7.1
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940 Componenti: Chromosome II

Organism-specific databases

WormBaseiR03D7.1; CE01609; WBGene00010988; metr-1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12491249Probable methionine synthasePRO_0000204531Add
BLAST

Proteomic databases

PaxDbiQ09582.
PRIDEiQ09582.

Interactioni

Protein-protein interaction databases

BioGridi39991. 1 interaction.
DIPiDIP-26122N.
IntActiQ09582. 1 interaction.
MINTiMINT-1116270.
STRINGi6239.R03D7.1.

Structurei

3D structure databases

ProteinModelPortaliQ09582.
SMRiQ09582. Positions 5-640.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 327327Hcy-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini360 – 621262Pterin-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini652 – 74998B12-binding N-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini762 – 897136B12-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini913 – 1249337AdoMet activationPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni850 – 8512Cobalamin-bindingBy similarity
Regioni1211 – 12122S-adenosyl-L-methionine bindingBy similarity

Domaini

Modular enzyme with four functionally distinct domains. The isolated Hcy-binding domain catalyzes methyl transfer from free methylcobalamin to homocysteine. The Hcy-binding domain in association with the pterin-binding domain catalyzes the methylation of cob(I)alamin by methyltetrahydrofolate and the methylation of homocysteine. The B12-binding domain binds the cofactor. The AdoMet activation domain binds S-adenosyl-L-methionine. Under aerobic conditions cob(I)alamin can be converted to inactive cob(II)alamin. Reductive methylation by S-adenosyl-L-methionine and flavodoxin regenerates methylcobalamin (By similarity).By similarity

Sequence similaritiesi

Contains 1 AdoMet activation domain.PROSITE-ProRule annotation
Contains 1 B12-binding domain.PROSITE-ProRule annotation
Contains 1 Hcy-binding domain.PROSITE-ProRule annotation
Contains 1 pterin-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1410.
GeneTreeiENSGT00420000029824.
HOGENOMiHOG000251409.
InParanoidiQ09582.
KOiK00548.
OMAiDYNSIMV.
OrthoDBiEOG7TF786.
PhylomeDBiQ09582.

Family and domain databases

Gene3Di1.10.1240.10. 1 hit.
3.10.196.10. 1 hit.
3.20.20.20. 1 hit.
3.20.20.330. 1 hit.
3.40.50.280. 1 hit.
InterProiIPR003759. Cbl-bd_cap.
IPR006158. Cobalamin-bd.
IPR011005. Dihydropteroate_synth-like.
IPR011822. MetH.
IPR000489. Pterin-binding.
IPR003726. S_MeTrfase.
IPR004223. VitB12-dep_Met_synth_activ_dom.
[Graphical view]
PfamiPF02310. B12-binding. 1 hit.
PF02607. B12-binding_2. 1 hit.
PF02965. Met_synt_B12. 1 hit.
PF00809. Pterin_bind. 1 hit.
PF02574. S-methyl_trans. 1 hit.
[Graphical view]
PIRSFiPIRSF000381. MetH. 1 hit.
SMARTiSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMiSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsiTIGR02082. metH. 1 hit.
PROSITEiPS50974. ADOMET_ACTIVATION. 1 hit.
PS51332. B12_BINDING. 1 hit.
PS51337. B12_BINDING_NTER. 1 hit.
PS50970. HCY. 1 hit.
PS50972. PTERIN_BINDING. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q09582-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRSSLFEEL AEIAKERIMI IDGAMGTMIQ REYMEEEDFR GEILKDHDKP
60 70 80 90 100
LKGNNDLLSI TRPDIIYKIH KLYLEAGADF VETNTFSGTT IAQADYRCEH
110 120 130 140 150
LVHEINYQSA LVARRACDDV GAATGRRRYV CGAIGPTNRT LSISPSVEKP
160 170 180 190 200
DFRNVTFQEL VKAYGDQARS LIQGGVDVLL VETVFDSANA KAALFAIRTL
210 220 230 240 250
FEDEGVPEMP VFLSGTIVDM SGRTLSGQTG EAFLVSTKQG KPMAVGLNCA
260 270 280 290 300
LGAKDMRQFV DNMSKWSDSF IICYPNAGLP NALGGYDETP EEMADVLREF
310 320 330 340 350
ARDGLVNIIG GCCGTTPDHI NAMYKAVQGI TPRVPPQDPH AGKMLLSGLE
360 370 380 390 400
PSIVGPETNF VNIGERCNVA GSRRFCNLIK NENYDTAIDV ARVQVDSGAQ
410 420 430 440 450
ILDVNMDDGL LDGPYAMSKF LRLISSEPDV AKIPVCIDSS DFDVIIAGLE
460 470 480 490 500
STQGKCVVNS ISLKEGEEKF KERARIIKRY GAAVVVMAFD EQGQAAETDP
510 520 530 540 550
KFEICERSYR ILTEEVGFNP NDIIFDANIL TIATGMEEHS NYGMYFIEAA
560 570 580 590 600
RMIRENLPGA HVSGGVSNIS FSFRGMEAIR EAMHSVFLFY AIKAGMDMGI
610 620 630 640 650
VNAGALPVYE DIDKPLLQLL EDLLFNRDPE ATEKLLVAAQ EMKKDGKKAD
660 670 680 690 700
TKTDEWRSLT VEERLKFALV KGVDQFVVAD TEEARQNTAK YPRPLNVIER
710 720 730 740 750
PLMDGMAVVG ELFGAGKMFL PQVIKSARVM KKAVAHLLPF MEIERQANIE
760 770 780 790 800
TMGLAEDESP YQGTVVIATV KGDVHDIGKN IVSVVLGCNN FKVVDLGVMT
810 820 830 840 850
PCENIIKAAI EEKADFIGLS GLITPSLDEM VYVAKEMNRV GLNIPLLIGG
860 870 880 890 900
ATTSKTHTAV KISPRYPHPV VHCLDASKSV VVCSSLSDMS VRDAFLQDLN
910 920 930 940 950
EDYEDVRQEH YASLKDRRFT DLNKTREKKF KIDWDKFTAV KPSFVGRREY
960 970 980 990 1000
QNFDLNELIP YIDWKPFFDV WQLRGKYPNR SYPKIFDDAD VGAEAKKVFD
1010 1020 1030 1040 1050
DAQTWLKKLI DEKILVANAV VSFLPAASEG DDMHVYDPET GNKLDTFYGL
1060 1070 1080 1090 1100
RQQSGREHDQ PHFCLSDFIK PLKNGVPDDY LGLFACTAGL GAEEYCKTLE
1110 1120 1130 1140 1150
KNHDDYASIM VKALADRLAE AYAEYLHKEV RTTLWGYSTN EDLTESDLLS
1160 1170 1180 1190 1200
IKYQGIRPAC GYPSQPDHTE KRTLWKLLEA EKNGIGLTEH LAMLPAASVS
1210 1220 1230 1240
GLYFANPQSE YFAVGKIDQD QVIDYAARKN VPKEEVERWL SPILGYDTD
Length:1,249
Mass (Da):138,899
Last modified:November 1, 1996 - v1
Checksum:i4D16028AD02CD550
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46828 Genomic DNA. Translation: CAA86855.1.
PIRiT23868.
RefSeqiNP_496353.1. NM_063952.4.
UniGeneiCel.16853.

Genome annotation databases

EnsemblMetazoaiR03D7.1; R03D7.1; WBGene00010988.
GeneIDi174681.
KEGGicel:CELE_R03D7.1.
UCSCiR03D7.1. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46828 Genomic DNA. Translation: CAA86855.1.
PIRiT23868.
RefSeqiNP_496353.1. NM_063952.4.
UniGeneiCel.16853.

3D structure databases

ProteinModelPortaliQ09582.
SMRiQ09582. Positions 5-640.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi39991. 1 interaction.
DIPiDIP-26122N.
IntActiQ09582. 1 interaction.
MINTiMINT-1116270.
STRINGi6239.R03D7.1.

Proteomic databases

PaxDbiQ09582.
PRIDEiQ09582.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiR03D7.1; R03D7.1; WBGene00010988.
GeneIDi174681.
KEGGicel:CELE_R03D7.1.
UCSCiR03D7.1. c. elegans.

Organism-specific databases

CTDi174681.
WormBaseiR03D7.1; CE01609; WBGene00010988; metr-1.

Phylogenomic databases

eggNOGiCOG1410.
GeneTreeiENSGT00420000029824.
HOGENOMiHOG000251409.
InParanoidiQ09582.
KOiK00548.
OMAiDYNSIMV.
OrthoDBiEOG7TF786.
PhylomeDBiQ09582.

Enzyme and pathway databases

UniPathwayiUPA00051; UER00081.
ReactomeiREACT_274901. Methylation.
REACT_320610. Sulfur amino acid metabolism.
REACT_347550. Cobalamin (Cbl, vitamin B12) transport and metabolism.

Miscellaneous databases

NextBioi885042.
PROiQ09582.

Family and domain databases

Gene3Di1.10.1240.10. 1 hit.
3.10.196.10. 1 hit.
3.20.20.20. 1 hit.
3.20.20.330. 1 hit.
3.40.50.280. 1 hit.
InterProiIPR003759. Cbl-bd_cap.
IPR006158. Cobalamin-bd.
IPR011005. Dihydropteroate_synth-like.
IPR011822. MetH.
IPR000489. Pterin-binding.
IPR003726. S_MeTrfase.
IPR004223. VitB12-dep_Met_synth_activ_dom.
[Graphical view]
PfamiPF02310. B12-binding. 1 hit.
PF02607. B12-binding_2. 1 hit.
PF02965. Met_synt_B12. 1 hit.
PF00809. Pterin_bind. 1 hit.
PF02574. S-methyl_trans. 1 hit.
[Graphical view]
PIRSFiPIRSF000381. MetH. 1 hit.
SMARTiSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMiSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsiTIGR02082. metH. 1 hit.
PROSITEiPS50974. ADOMET_ACTIVATION. 1 hit.
PS51332. B12_BINDING. 1 hit.
PS51337. B12_BINDING_NTER. 1 hit.
PS50970. HCY. 1 hit.
PS50972. PTERIN_BINDING. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.

Entry informationi

Entry nameiMETH_CAEEL
AccessioniPrimary (citable) accession number: Q09582
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: June 24, 2015
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Miscellaneous

L-homocysteine is bound via the zinc atom.By similarity

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.