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Q54P92

- METH_DICDI

UniProt

Q54P92 - METH_DICDI

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Protein

Methionine synthase

Gene

mtr

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - 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:

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
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.
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.
InParanoidiQ54P92.
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

        10         20         30         40         50
MINSNDKNES DTFGIIRKIL SERIMVLDGA MGTEIQKFKL KDNDYRGEEF
60 70 80 90 100
KDFPHELGGN NDLLSLTQPH IIREIHCKYL EAGADFIETN TFNGNIFSQA
110 120 130 140 150
DYKMEHLVKR INIESARLAK SACEEYTKKD PSRPRFVCGA VGPTNKTASI
160 170 180 190 200
SPSVERPEAR NVLFDELVSG YLEQVEALVE GGIDVILVET VFDSLNCKAA
210 220 230 240 250
LFAIEEFFKT YSPRLPVFVS GTIVDKSGRT LSGQTGEAFY TSVASANLMV
260 270 280 290 300
FGLNCALGAQ EMRPFLQNIS KCSECYVSCY PNAGLPNTFG GYDETPEMMA
310 320 330 340 350
EQIKEFAESG LLNIVGGCCG TSPDHIRAFC NAIEGIAPRA IPTLVPNTTL
360 370 380 390 400
SGLEPLVFTK ELNFVNVGER CNVSGSRRFA NLIKANKYEE ALSVARQQVE
410 420 430 440 450
AGAQIIDINM DEGMIDAVAA IQKFLFFIGS EPEISKVPIM LDSSNFDVVE
460 470 480 490 500
AGLKCVQGKC IVNSISLKVG EELFIKQAKI VKQYGASVVV MAFDENGQAT
510 520 530 540 550
SKEEKVRICY RSYKILTEQV GFYPQDIIFD PNILTIATGL EEHNNYGVEF
560 570 580 590 600
IEATREIKAL MPLTRVSGGV SNLSFSFRGN EPLREAMHSA FLYYAIAAGM
610 620 630 640 650
DMGIVNAGAL PIYDDIPKDL LKLVEDAILN RTNDATEKLL EYAQANNKSE
660 670 680 690 700
KANVEVEEWR NKPVSERIAH ALVKGITTYI IEDTEEARNT LPSSLSVIEG
710 720 730 740 750
PLMGGMNVVG DLFGAGKMFL PQVIKSARVM KKAVAHLIPF MEEEKRLKRL
760 770 780 790 800
EKGNDEAAED EPDNAGVVVL ATVKGDVHDI GKNIVGVVLG CNNYKVIDIG
810 820 830 840 850
VMTPCEKIVE AIIANKADVV GLSGLITPSL DEMIYVASEL ERLKFKIPLM
860 870 880 890 900
IGGATTSQIH TAVKISPHYS QPTVHVLDAS RSVTVVQSLL DPNNKEVFAE
910 920 930 940 950
DVSQQYAELR EKHYASLKDR KYTSLEKARQ HCVKVNWKTI QPVKPTFLGT
960 970 980 990 1000
QVFKEYSLEK LVTKIDWNPF FVTWQLRGKY PNRGYPRIFN DETVGAEAKK
1010 1020 1030 1040 1050
LFDDAQTMLK EIVDKKLLNA RGVIGFYPAN SIDEDIIIYD HNDDETRSKP
1060 1070 1080 1090 1100
IATLFGLRQQ NEKETDEPYI AIGDYIAPVS SGVKDYIGLF AVSSGFGLED
1110 1120 1130 1140 1150
MVEKYKKEND DYSSIMAKAL ADRLAEALAE AVHEDVRREH WAYEKDQALS
1160 1170 1180 1190 1200
NEDLFKIKYK GIRPAPGYPA QPDHTEMKTI WSLMNVNENT SIELTDHMAM
1210 1220 1230 1240 1250
LPGAAVCGVY FSHEHAKYFS VGKITKEQIE SYASRKQITK EEAERWLSSI
1260
LSYDRLPLVK
Length:1,260
Mass (Da):140,122
Last modified:May 24, 2005 - v1
Checksum:i095402C1F5889CF0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi Q54P92.
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: November 26, 2014
This is version 66 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