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Protein

Methionine synthase

Gene

Mtr

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

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:iL-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. Methionine synthase (Mtr)
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 bindingi248 – 2481ZincPROSITE-ProRule annotation
Metal bindingi311 – 3111ZincPROSITE-ProRule annotation
Metal bindingi312 – 3121ZincPROSITE-ProRule annotation
Metal bindingi773 – 7731Cobalt (cobalamin axial ligand)By similarity
Binding sitei818 – 8181CobalaminBy similarity
Binding sitei962 – 9621S-adenosyl-L-methionineBy similarity
Binding sitei1160 – 11601S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei1164 – 11641Cobalamin; via carbonyl oxygenBy similarity

GO - Molecular functioni

  • amino acid binding Source: RGD
  • cobalamin binding Source: RGD
  • folic acid binding Source: RGD
  • methionine synthase activity Source: RGD
  • methyltransferase activity Source: RGD
  • S-adenosylmethionine-homocysteine S-methyltransferase activity Source: InterPro
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cellular response to methionine Source: RGD
  • homocysteine metabolic process Source: RGD
  • methionine biosynthetic process Source: RGD
  • methionine metabolic process Source: RGD
  • protein methylation Source: RGD
  • tetrahydrofolate metabolic process Source: RGD
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
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621283. Mtr.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12531253Methionine synthasePRO_0000312902Add
BLAST

Proteomic databases

PaxDbiQ9Z2Q4.
PRIDEiQ9Z2Q4.

PTM databases

PhosphoSiteiQ9Z2Q4.

Expressioni

Gene expression databases

GenevisibleiQ9Z2Q4. RN.

Interactioni

Protein-protein interaction databases

BioGridi249519. 1 interaction.
IntActiQ9Z2Q4. 1 interaction.
STRINGi10116.ENSRNOP00000023973.

Structurei

3D structure databases

ProteinModelPortaliQ9Z2Q4.
SMRiQ9Z2Q4. Positions 652-908, 914-1252.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 326321Hcy-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini359 – 620262Pterin-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini650 – 74798B12-binding N-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini760 – 895136B12-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini911 – 1253343AdoMet activationPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni848 – 8492Cobalamin-bindingBy similarity
Regioni1215 – 12162S-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.
HOGENOMiHOG000251409.
HOVERGENiHBG006347.
InParanoidiQ9Z2Q4.
KOiK00548.
PhylomeDBiQ9Z2Q4.

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.

Q9Z2Q4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKTLQDEIE AILRKRIMVL DGGMGTMIQR YKLSEENFQG QEFKDHSRPL
60 70 80 90 100
KGNNDILSIT QPDVIYQIHK EYLLAGADII ETNTFSSTSI AQADYGLEHL
110 120 130 140 150
AYRMNKCSAD VARKAAEEIT LQTGVKRFVA GSLGPTNKTL SVSPSVERPD
160 170 180 190 200
YRNITFDELV EAYQEQAKGL LDGGVDILLI ETIFDTANAK AALFALQKLF
210 220 230 240 250
EENYASPRPI FISGTIVDKS GRTLSGQTGE AFVTSVSHSD PLCIGLNCAL
260 270 280 290 300
GAAEMRPFIE TIGKCTTAYV LCYPNAGLPN TFGDYDETPA MMAMHLKDFA
310 320 330 340 350
VDGLVNVVGG CCGSTPDHIR EIAEAVKNCK PRVPPDSVFE GHMLLSGLEP
360 370 380 390 400
FRIGPYTNFV NIGERCNVAG SKKFAKLIMA GNYEEALSVA KVQVEMGAQV
410 420 430 440 450
LDINMDDGML DGPSAMTKFC NFIASEPDIA KVPLCIDSSN FAVIEAGLKC
460 470 480 490 500
CQGKCIVNSI SLKEGEEDFL EKARKIKKFG AAVVVMAFDE EGQATETDVK
510 520 530 540 550
VSVCTRAYHL LVEKVGFNPN DIIFDPNILT IGTGMEEHNL YAINFIHATR
560 570 580 590 600
VIKETLPGVR ISGGLSNLSF AFRGMDAIRE AMHGVFLYHA IKFGMDMGIV
610 620 630 640 650
NAGSLPVYDD IHKDLLQLCE DLIWNRDAEA TEKLLRYAQT HGKGGKKVIQ
660 670 680 690 700
TDEWRNGSIE ERLEYALVKG IEKHIVEDTE EARLNREKYP RPLNIIEGPL
710 720 730 740 750
MNGMKVVGDL FGAGKMFLPQ VIKSARVMKK AVGHLIPFME KEREEARVLN
760 770 780 790 800
GSVEEEDPYQ GTIVLATVKG DVHDIGKNIV GVVLGCNNFR VIDLGVMTPC
810 820 830 840 850
DKILQAALDH KADIIGLSGL ITPSLDEMIF VAKEMERLAI KIPLLIGGAT
860 870 880 890 900
TSRTHTAVKI APRYSAPVIH VLDASKSVVV CSQLLDENLK DDYFEEILEE
910 920 930 940 950
YEDIRQDHYE SLKERKYLPL SQARKHSFHI DWLSEPHPVK PTFIGTQVFE
960 970 980 990 1000
DYNLQKLVDY IDWKPFFDVW QLRGKYPNRG FPKIFNDKAV GEEARKVYED
1010 1020 1030 1040 1050
AQNMLSILIS RKKLRARGVV GFWPAQSVQD DIHLYAEGAV PQAAEPIATF
1060 1070 1080 1090 1100
YGLRQQAEKD SSSTDPYHCL SDFVAPLHSG VRDYLGLFAV ACFGVEELSK
1110 1120 1130 1140 1150
AYEDDGDDYS SIMVKALGDR LAEAFAEELH ERVRRELWAY CGSEQLGVTD
1160 1170 1180 1190 1200
LRKLRYEGIR PAPGYPSQPD HTEKLTMWRL ANIEQATGIR LTESLAMAPA
1210 1220 1230 1240 1250
SAVSGLYFSN VKSKYFAVGK ISKDQIEDYA LRKNMSVAEV EKWLGPILGY

DTD
Length:1,253
Mass (Da):139,164
Last modified:May 1, 1999 - v1
Checksum:i96BD40B796EBD75B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF034214 mRNA. Translation: AAD05384.1.
PIRiT42376.
RefSeqiNP_110491.1. NM_030864.1.
UniGeneiRn.205061.

Genome annotation databases

GeneIDi81522.
KEGGirno:81522.
UCSCiRGD:621283. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF034214 mRNA. Translation: AAD05384.1.
PIRiT42376.
RefSeqiNP_110491.1. NM_030864.1.
UniGeneiRn.205061.

3D structure databases

ProteinModelPortaliQ9Z2Q4.
SMRiQ9Z2Q4. Positions 652-908, 914-1252.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249519. 1 interaction.
IntActiQ9Z2Q4. 1 interaction.
STRINGi10116.ENSRNOP00000023973.

PTM databases

PhosphoSiteiQ9Z2Q4.

Proteomic databases

PaxDbiQ9Z2Q4.
PRIDEiQ9Z2Q4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi81522.
KEGGirno:81522.
UCSCiRGD:621283. rat.

Organism-specific databases

CTDi4548.
RGDi621283. Mtr.

Phylogenomic databases

eggNOGiCOG1410.
HOGENOMiHOG000251409.
HOVERGENiHBG006347.
InParanoidiQ9Z2Q4.
KOiK00548.
PhylomeDBiQ9Z2Q4.

Enzyme and pathway databases

UniPathwayiUPA00051; UER00081.

Miscellaneous databases

NextBioi615041.
PROiQ9Z2Q4.

Gene expression databases

GenevisibleiQ9Z2Q4. RN.

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. "Cloning, sequencing, and heterologous expression of rat methionine synthase cDNA."
    Yamada K., Tobimatsu T., Toraya T.
    Biosci. Biotechnol. Biochem. 62:2155-2160(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Wistar.
    Tissue: Liver.

Entry informationi

Entry nameiMETH_RAT
AccessioniPrimary (citable) accession number: Q9Z2Q4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 1, 1999
Last modified: June 24, 2015
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.