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Q54P92

- METH_DICDI

UniProt

Q54P92 - METH_DICDI

Protein

Methionine synthase

Gene

mtr

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      Previous versions | rss
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    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

    Methylcobalamin (MeCBL).By similarity
    Binds 1 zinc ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi255 – 2551ZincPROSITE-ProRule annotation
    Metal bindingi318 – 3181ZincPROSITE-ProRule annotation
    Metal bindingi319 – 3191ZincPROSITE-ProRule annotation
    Metal bindingi778 – 7781Cobalt (cobalamin axial ligand)By similarity
    Binding sitei823 – 8231CobalaminBy similarity
    Binding sitei966 – 9661S-adenosyl-L-methionineBy similarity
    Binding sitei1163 – 11631S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
    Binding sitei1167 – 11671Cobalamin; via carbonyl oxygenBy similarity

    GO - Molecular functioni

    1. cobalamin binding Source: UniProtKB-KW
    2. methionine synthase activity Source: UniProtKB
    3. S-adenosylmethionine-homocysteine S-methyltransferase activity Source: InterPro
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. methionine biosynthetic process Source: UniProtKB
    2. pteridine-containing compound metabolic process Source: InterPro

    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

    UniPathwayiUPA00051; UER00081.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    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:mtr
    ORF Names:DDB_G0284699
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 4, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0284699. mtr.

    Subcellular locationi

    GO - Cellular componenti

    1. intracellular Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12601260Methionine synthasePRO_0000327799Add
    BLAST

    Proteomic databases

    PRIDEiQ54P92.

    Interactioni

    Protein-protein interaction databases

    STRINGi44689.DDB_0230138.

    Structurei

    3D structure databases

    ProteinModelPortaliQ54P92.
    SMRiQ54P92. Positions 657-913, 919-1254.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini13 – 333321Hcy-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini364 – 625262Pterin-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini655 – 74995B12-binding N-terminalPROSITE-ProRule annotationAdd
    BLAST
    Domaini766 – 883118B12-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini916 – 1256341AdoMet activationPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni853 – 8542Cobalamin-bindingBy similarity
    Regioni1218 – 12192S-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.
    KOiK00548.
    OMAiEEIHARY.
    PhylomeDBiQ54P92.

    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.

    Q54P92-1 [UniParc]FASTAAdd to Basket

    « Hide

    MINSNDKNES DTFGIIRKIL SERIMVLDGA MGTEIQKFKL KDNDYRGEEF     50
    KDFPHELGGN NDLLSLTQPH IIREIHCKYL EAGADFIETN TFNGNIFSQA 100
    DYKMEHLVKR INIESARLAK SACEEYTKKD PSRPRFVCGA VGPTNKTASI 150
    SPSVERPEAR NVLFDELVSG YLEQVEALVE GGIDVILVET VFDSLNCKAA 200
    LFAIEEFFKT YSPRLPVFVS GTIVDKSGRT LSGQTGEAFY TSVASANLMV 250
    FGLNCALGAQ EMRPFLQNIS KCSECYVSCY PNAGLPNTFG GYDETPEMMA 300
    EQIKEFAESG LLNIVGGCCG TSPDHIRAFC NAIEGIAPRA IPTLVPNTTL 350
    SGLEPLVFTK ELNFVNVGER CNVSGSRRFA NLIKANKYEE ALSVARQQVE 400
    AGAQIIDINM DEGMIDAVAA IQKFLFFIGS EPEISKVPIM LDSSNFDVVE 450
    AGLKCVQGKC IVNSISLKVG EELFIKQAKI VKQYGASVVV MAFDENGQAT 500
    SKEEKVRICY RSYKILTEQV GFYPQDIIFD PNILTIATGL EEHNNYGVEF 550
    IEATREIKAL MPLTRVSGGV SNLSFSFRGN EPLREAMHSA FLYYAIAAGM 600
    DMGIVNAGAL PIYDDIPKDL LKLVEDAILN RTNDATEKLL EYAQANNKSE 650
    KANVEVEEWR NKPVSERIAH ALVKGITTYI IEDTEEARNT LPSSLSVIEG 700
    PLMGGMNVVG DLFGAGKMFL PQVIKSARVM KKAVAHLIPF MEEEKRLKRL 750
    EKGNDEAAED EPDNAGVVVL ATVKGDVHDI GKNIVGVVLG CNNYKVIDIG 800
    VMTPCEKIVE AIIANKADVV GLSGLITPSL DEMIYVASEL ERLKFKIPLM 850
    IGGATTSQIH TAVKISPHYS QPTVHVLDAS RSVTVVQSLL DPNNKEVFAE 900
    DVSQQYAELR EKHYASLKDR KYTSLEKARQ HCVKVNWKTI QPVKPTFLGT 950
    QVFKEYSLEK LVTKIDWNPF FVTWQLRGKY PNRGYPRIFN DETVGAEAKK 1000
    LFDDAQTMLK EIVDKKLLNA RGVIGFYPAN SIDEDIIIYD HNDDETRSKP 1050
    IATLFGLRQQ NEKETDEPYI AIGDYIAPVS SGVKDYIGLF AVSSGFGLED 1100
    MVEKYKKEND DYSSIMAKAL ADRLAEALAE AVHEDVRREH WAYEKDQALS 1150
    NEDLFKIKYK GIRPAPGYPA QPDHTEMKTI WSLMNVNENT SIELTDHMAM 1200
    LPGAAVCGVY FSHEHAKYFS VGKITKEQIE SYASRKQITK EEAERWLSSI 1250
    LSYDRLPLVK 1260
    Length:1,260
    Mass (Da):140,122
    Last modified:May 24, 2005 - v1
    Checksum:i095402C1F5889CF0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000070 Genomic DNA. Translation: EAL65119.1.
    RefSeqiXP_638483.1. XM_633391.1.

    Genome annotation databases

    EnsemblProtistsiDDB0230138; DDB0230138; DDB_G0284699.
    GeneIDi8624734.
    KEGGiddi:DDB_G0284699.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000070 Genomic DNA. Translation: EAL65119.1 .
    RefSeqi XP_638483.1. XM_633391.1.

    3D structure databases

    ProteinModelPortali Q54P92.
    SMRi Q54P92. Positions 657-913, 919-1254.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0230138.

    Proteomic databases

    PRIDEi Q54P92.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0230138 ; DDB0230138 ; DDB_G0284699 .
    GeneIDi 8624734.
    KEGGi ddi:DDB_G0284699.

    Organism-specific databases

    dictyBasei DDB_G0284699. mtr.

    Phylogenomic databases

    eggNOGi COG1410.
    KOi K00548.
    OMAi EEIHARY.
    PhylomeDBi Q54P92.

    Enzyme and pathway databases

    UniPathwayi UPA00051 ; UER00081 .

    Miscellaneous databases

    PROi Q54P92.

    Family and domain databases

    Gene3Di 1.10.1240.10. 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.
    InterProi IPR003759. 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 ]
    Pfami PF02310. 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 ]
    PIRSFi PIRSF000381. MetH. 1 hit.
    SMARTi SM01018. B12-binding_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47644. SSF47644. 1 hit.
    SSF51717. SSF51717. 1 hit.
    SSF52242. SSF52242. 1 hit.
    SSF56507. SSF56507. 1 hit.
    SSF82282. SSF82282. 1 hit.
    TIGRFAMsi TIGR02082. metH. 1 hit.
    PROSITEi PS50974. 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 ]
    ProtoNeti Search...

    Publicationsi

    1. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.

    Entry informationi

    Entry nameiMETH_DICDI
    AccessioniPrimary (citable) accession number: Q54P92
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 8, 2008
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 64 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Miscellaneous

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

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3