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Q54P92 (METH_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 62. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Methionine synthase

EC=2.1.1.13
Alternative name(s):
5-methyltetrahydrofolate--homocysteine methyltransferase
Vitamin-B12 dependent methionine synthase
Short name=MS
Gene names
Name:mtr
ORF Names:DDB_G0284699
OrganismDictyostelium discoideum (Slime mold) [Reference proteome]
Taxonomic identifier44689 [NCBI]
Taxonomic lineageEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium

Protein attributes

Sequence length1260 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 activity

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

Cofactor

Methylcobalamin (MeCBL) By similarity.

Binds 1 zinc ion per subunit By similarity.

Pathway

Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetH route): step 1/1.

Domain

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.

Miscellaneous

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

Sequence similarities

Belongs to the vitamin-B12 dependent methionine synthase family.

Contains 1 AdoMet activation domain.

Contains 1 B12-binding domain.

Contains 1 B12-binding N-terminal domain.

Contains 1 Hcy-binding domain.

Contains 1 pterin-binding domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12601260Methionine synthase
PRO_0000327799

Regions

Domain13 – 333321Hcy-binding
Domain364 – 625262Pterin-binding
Domain655 – 74995B12-binding N-terminal
Domain766 – 883118B12-binding
Domain916 – 1256341AdoMet activation
Region853 – 8542Cobalamin-binding By similarity
Region1218 – 12192S-adenosyl-L-methionine binding By similarity

Sites

Metal binding2551Zinc By similarity
Metal binding3181Zinc By similarity
Metal binding3191Zinc By similarity
Metal binding7781Cobalt (cobalamin axial ligand) By similarity
Binding site8231Cobalamin By similarity
Binding site9661S-adenosyl-L-methionine By similarity
Binding site11631S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding site11671Cobalamin; via carbonyl oxygen By similarity

Sequences

Sequence LengthMass (Da)Tools
Q54P92 [UniParc].

Last modified May 24, 2005. Version 1.
Checksum: 095402C1F5889CF0

FASTA1,260140,122
        10         20         30         40         50         60 
MINSNDKNES DTFGIIRKIL SERIMVLDGA MGTEIQKFKL KDNDYRGEEF KDFPHELGGN 

        70         80         90        100        110        120 
NDLLSLTQPH IIREIHCKYL EAGADFIETN TFNGNIFSQA DYKMEHLVKR INIESARLAK 

       130        140        150        160        170        180 
SACEEYTKKD PSRPRFVCGA VGPTNKTASI SPSVERPEAR NVLFDELVSG YLEQVEALVE 

       190        200        210        220        230        240 
GGIDVILVET VFDSLNCKAA LFAIEEFFKT YSPRLPVFVS GTIVDKSGRT LSGQTGEAFY 

       250        260        270        280        290        300 
TSVASANLMV FGLNCALGAQ EMRPFLQNIS KCSECYVSCY PNAGLPNTFG GYDETPEMMA 

       310        320        330        340        350        360 
EQIKEFAESG LLNIVGGCCG TSPDHIRAFC NAIEGIAPRA IPTLVPNTTL SGLEPLVFTK 

       370        380        390        400        410        420 
ELNFVNVGER CNVSGSRRFA NLIKANKYEE ALSVARQQVE AGAQIIDINM DEGMIDAVAA 

       430        440        450        460        470        480 
IQKFLFFIGS EPEISKVPIM LDSSNFDVVE AGLKCVQGKC IVNSISLKVG EELFIKQAKI 

       490        500        510        520        530        540 
VKQYGASVVV MAFDENGQAT SKEEKVRICY RSYKILTEQV GFYPQDIIFD PNILTIATGL 

       550        560        570        580        590        600 
EEHNNYGVEF IEATREIKAL MPLTRVSGGV SNLSFSFRGN EPLREAMHSA FLYYAIAAGM 

       610        620        630        640        650        660 
DMGIVNAGAL PIYDDIPKDL LKLVEDAILN RTNDATEKLL EYAQANNKSE KANVEVEEWR 

       670        680        690        700        710        720 
NKPVSERIAH ALVKGITTYI IEDTEEARNT LPSSLSVIEG PLMGGMNVVG DLFGAGKMFL 

       730        740        750        760        770        780 
PQVIKSARVM KKAVAHLIPF MEEEKRLKRL EKGNDEAAED EPDNAGVVVL ATVKGDVHDI 

       790        800        810        820        830        840 
GKNIVGVVLG CNNYKVIDIG VMTPCEKIVE AIIANKADVV GLSGLITPSL DEMIYVASEL 

       850        860        870        880        890        900 
ERLKFKIPLM IGGATTSQIH TAVKISPHYS QPTVHVLDAS RSVTVVQSLL DPNNKEVFAE 

       910        920        930        940        950        960 
DVSQQYAELR EKHYASLKDR KYTSLEKARQ HCVKVNWKTI QPVKPTFLGT QVFKEYSLEK 

       970        980        990       1000       1010       1020 
LVTKIDWNPF FVTWQLRGKY PNRGYPRIFN DETVGAEAKK LFDDAQTMLK EIVDKKLLNA 

      1030       1040       1050       1060       1070       1080 
RGVIGFYPAN SIDEDIIIYD HNDDETRSKP IATLFGLRQQ NEKETDEPYI AIGDYIAPVS 

      1090       1100       1110       1120       1130       1140 
SGVKDYIGLF AVSSGFGLED MVEKYKKEND DYSSIMAKAL ADRLAEALAE AVHEDVRREH 

      1150       1160       1170       1180       1190       1200 
WAYEKDQALS NEDLFKIKYK GIRPAPGYPA QPDHTEMKTI WSLMNVNENT SIELTDHMAM 

      1210       1220       1230       1240       1250       1260 
LPGAAVCGVY FSHEHAKYFS VGKITKEQIE SYASRKQITK EEAERWLSSI LSYDRLPLVK 

« Hide

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AAFI02000070 Genomic DNA. Translation: EAL65119.1.
RefSeqXP_638483.1. XM_633391.1.

3D structure databases

ProteinModelPortalQ54P92.
SMRQ54P92. Positions 657-913, 919-1254.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING44689.DDB_0230138.

Proteomic databases

PRIDEQ54P92.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsDDB0230138; DDB0230138; DDB_G0284699.
GeneID8624734.
KEGGddi:DDB_G0284699.

Organism-specific databases

dictyBaseDDB_G0284699. mtr.

Phylogenomic databases

eggNOGCOG1410.
OMAEEIHARY.
PhylomeDBQ54P92.

Enzyme and pathway databases

UniPathwayUPA00051; UER00081.

Family and domain databases

Gene3D1.10.1240.10. 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.
InterProIPR003759. 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]
PfamPF02310. 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]
PIRSFPIRSF000381. MetH. 1 hit.
SMARTSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsTIGR02082. metH. 1 hit.
PROSITEPS50974. 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]
ProtoNetSearch...

Other

PROQ54P92.

Entry information

Entry nameMETH_DICDI
AccessionPrimary (citable) accession number: Q54P92
Entry history
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: May 24, 2005
Last modified: July 9, 2014
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase