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Q54P92

- METH_DICDI

UniProt

Q54P92 - METH_DICDI

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Protein

Methionine synthase

Gene
mtr, DDB_G0284699
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 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.

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 – 2551Zinc By similarity
Metal bindingi318 – 3181Zinc By similarity
Metal bindingi319 – 3191Zinc By similarity
Metal bindingi778 – 7781Cobalt (cobalamin axial ligand) By similarity
Binding sitei823 – 8231Cobalamin By similarity
Binding sitei966 – 9661S-adenosyl-L-methionine By similarity
Binding sitei1163 – 11631S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding sitei1167 – 11671Cobalamin; via carbonyl oxygen By 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
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

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
Complete GO annotation...

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 333321Hcy-bindingAdd
BLAST
Domaini364 – 625262Pterin-bindingAdd
BLAST
Domaini655 – 74995B12-binding N-terminalAdd
BLAST
Domaini766 – 883118B12-bindingAdd
BLAST
Domaini916 – 1256341AdoMet activationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni853 – 8542Cobalamin-binding By similarity
Regioni1218 – 12192S-adenosyl-L-methionine binding By 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.

Sequence similaritiesi

Contains 1 B12-binding domain.
Contains 1 Hcy-binding domain.

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: September 3, 2014
This is version 63 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

Similar proteinsi