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Methionine synthase (EC 2.1.1.13) (5-methyltetrahydrofolate--homocysteine methyltransferase) (Vitamin-B12 dependent methionine synthase) (MS)

 METH_RAT                Reviewed;        1253 AA.
Q9Z2Q4;
15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
01-MAY-1999, sequence version 1.
23-MAY-2018, entry version 119.
RecName: Full=Methionine synthase;
EC=2.1.1.13;
AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase;
AltName: Full=Vitamin-B12 dependent methionine synthase;
Short=MS;
Name=Mtr;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=Wistar; TISSUE=Liver;
PubMed=9972236; DOI=10.1271/bbb.62.2155;
Yamada K., Tobimatsu T., Toraya T.;
"Cloning, sequencing, and heterologous expression of rat methionine
synthase cDNA.";
Biosci. Biotechnol. Biochem. 62:2155-2160(1998).
[2]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1252, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22673903; DOI=10.1038/ncomms1871;
Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A.,
Lundby C., Olsen J.V.;
"Quantitative maps of protein phosphorylation sites across 14
different rat organs and tissues.";
Nat. Commun. 3:876-876(2012).
-!- 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). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: 5-methyltetrahydrofolate + L-homocysteine =
tetrahydrofolate + L-methionine.
-!- COFACTOR:
Name=methylcob(III)alamin; Xref=ChEBI:CHEBI:28115;
Evidence={ECO:0000250};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Note=Binds 1 zinc ion per subunit. {ECO:0000250};
-!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de
novo pathway; L-methionine from L-homocysteine (MetH route): step
1/1.
-!- SUBUNIT: Monomer. Dimer. Mainly monomer. Interacts with MTRR.
{ECO:0000250|UniProtKB:Q99707}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
-!- 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). {ECO:0000250}.
-!- MISCELLANEOUS: L-homocysteine is bound via the zinc atom.
{ECO:0000250}.
-!- SIMILARITY: Belongs to the vitamin-B12 dependent methionine
synthase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF034214; AAD05384.1; -; mRNA.
PIR; T42376; T42376.
RefSeq; NP_110491.1; NM_030864.1.
UniGene; Rn.205061; -.
ProteinModelPortal; Q9Z2Q4; -.
SMR; Q9Z2Q4; -.
BioGrid; 249519; 1.
IntAct; Q9Z2Q4; 1.
STRING; 10116.ENSRNOP00000023973; -.
CarbonylDB; Q9Z2Q4; -.
iPTMnet; Q9Z2Q4; -.
PhosphoSitePlus; Q9Z2Q4; -.
PaxDb; Q9Z2Q4; -.
PRIDE; Q9Z2Q4; -.
GeneID; 81522; -.
KEGG; rno:81522; -.
UCSC; RGD:621283; rat.
CTD; 4548; -.
RGD; 621283; Mtr.
eggNOG; KOG1579; Eukaryota.
eggNOG; COG0646; LUCA.
eggNOG; COG1410; LUCA.
HOGENOM; HOG000251409; -.
HOVERGEN; HBG006347; -.
InParanoid; Q9Z2Q4; -.
KO; K00548; -.
PhylomeDB; Q9Z2Q4; -.
UniPathway; UPA00051; UER00081.
PRO; PR:Q9Z2Q4; -.
Proteomes; UP000002494; Unplaced.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0016597; F:amino acid binding; IDA:RGD.
GO; GO:0031419; F:cobalamin binding; TAS:RGD.
GO; GO:0005542; F:folic acid binding; IDA:RGD.
GO; GO:0008705; F:methionine synthase activity; IDA:RGD.
GO; GO:0008168; F:methyltransferase activity; IDA:RGD.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0061431; P:cellular response to methionine; IEP:RGD.
GO; GO:0050667; P:homocysteine metabolic process; IDA:RGD.
GO; GO:0009086; P:methionine biosynthetic process; IDA:RGD.
GO; GO:0006555; P:methionine metabolic process; IMP:RGD.
GO; GO:0006479; P:protein methylation; IDA:RGD.
GO; GO:0046653; P:tetrahydrofolate metabolic process; IDA:RGD.
CDD; cd02069; methionine_synthase_B12_BD; 1.
Gene3D; 1.10.1240.10; -; 1.
Gene3D; 3.10.196.10; -; 3.
Gene3D; 3.20.20.20; -; 1.
Gene3D; 3.20.20.330; -; 1.
InterPro; IPR003759; Cbl-bd_cap.
InterPro; IPR006158; Cobalamin-bd.
InterPro; IPR036724; Cobalamin-bd_sf.
InterPro; IPR011005; Dihydropteroate_synth-like.
InterPro; IPR003726; HCY_dom.
InterPro; IPR036589; HCY_dom_sf.
InterPro; IPR033706; Met_synthase_B12-bd.
InterPro; IPR011822; MetH.
InterPro; IPR036594; Meth_synthase_dom.
InterPro; IPR000489; Pterin-binding_dom.
InterPro; IPR004223; VitB12-dep_Met_synth_activ_dom.
InterPro; IPR037010; VitB12-dep_Met_synth_activ_sf.
Pfam; PF02310; B12-binding; 1.
Pfam; PF02607; B12-binding_2; 1.
Pfam; PF02965; Met_synt_B12; 1.
Pfam; PF00809; Pterin_bind; 1.
Pfam; PF02574; S-methyl_trans; 1.
PIRSF; PIRSF000381; MetH; 1.
SMART; SM01018; B12-binding_2; 1.
SUPFAM; SSF47644; SSF47644; 1.
SUPFAM; SSF51717; SSF51717; 1.
SUPFAM; SSF52242; SSF52242; 1.
SUPFAM; SSF56507; SSF56507; 1.
SUPFAM; SSF82282; SSF82282; 1.
TIGRFAMs; TIGR02082; metH; 1.
PROSITE; PS50974; ADOMET_ACTIVATION; 1.
PROSITE; PS51332; B12_BINDING; 1.
PROSITE; PS51337; B12_BINDING_NTER; 1.
PROSITE; PS50970; HCY; 1.
PROSITE; PS50972; PTERIN_BINDING; 1.
1: Evidence at protein level;
Amino-acid biosynthesis; Cobalamin; Cobalt; Complete proteome;
Cytoplasm; Metal-binding; Methionine biosynthesis; Methyltransferase;
Phosphoprotein; Reference proteome; Repeat; S-adenosyl-L-methionine;
Transferase; Zinc.
CHAIN 1 1253 Methionine synthase.
/FTId=PRO_0000312902.
DOMAIN 6 326 Hcy-binding. {ECO:0000255|PROSITE-
ProRule:PRU00333}.
DOMAIN 359 620 Pterin-binding. {ECO:0000255|PROSITE-
ProRule:PRU00334}.
DOMAIN 650 747 B12-binding N-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00667}.
DOMAIN 760 895 B12-binding. {ECO:0000255|PROSITE-
ProRule:PRU00666}.
DOMAIN 911 1253 AdoMet activation. {ECO:0000255|PROSITE-
ProRule:PRU00346}.
REGION 370 372 Substrate binding.
{ECO:0000250|UniProtKB:Q99707}.
REGION 848 849 Cobalamin-binding. {ECO:0000250}.
REGION 1215 1216 S-adenosyl-L-methionine binding.
{ECO:0000250}.
METAL 248 248 Zinc. {ECO:0000255|PROSITE-
ProRule:PRU00333}.
METAL 311 311 Zinc. {ECO:0000255|PROSITE-
ProRule:PRU00333}.
METAL 312 312 Zinc. {ECO:0000255|PROSITE-
ProRule:PRU00333}.
METAL 773 773 Cobalt (cobalamin axial ligand).
{ECO:0000250}.
BINDING 437 437 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 458 458 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 525 525 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 567 567 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 573 573 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 579 579 Substrate.
{ECO:0000250|UniProtKB:Q99707}.
BINDING 818 818 Cobalamin. {ECO:0000250}.
BINDING 962 962 S-adenosyl-L-methionine. {ECO:0000250}.
BINDING 1160 1160 S-adenosyl-L-methionine; via carbonyl
oxygen. {ECO:0000250}.
BINDING 1164 1164 Cobalamin; via carbonyl oxygen.
{ECO:0000250}.
MOD_RES 1252 1252 Phosphothreonine.
{ECO:0000244|PubMed:22673903}.
SEQUENCE 1253 AA; 139164 MW; 96BD40B796EBD75B CRC64;
MKKTLQDEIE AILRKRIMVL DGGMGTMIQR YKLSEENFQG QEFKDHSRPL KGNNDILSIT
QPDVIYQIHK EYLLAGADII ETNTFSSTSI AQADYGLEHL AYRMNKCSAD VARKAAEEIT
LQTGVKRFVA GSLGPTNKTL SVSPSVERPD YRNITFDELV EAYQEQAKGL LDGGVDILLI
ETIFDTANAK AALFALQKLF EENYASPRPI FISGTIVDKS GRTLSGQTGE AFVTSVSHSD
PLCIGLNCAL GAAEMRPFIE TIGKCTTAYV LCYPNAGLPN TFGDYDETPA MMAMHLKDFA
VDGLVNVVGG CCGSTPDHIR EIAEAVKNCK PRVPPDSVFE GHMLLSGLEP FRIGPYTNFV
NIGERCNVAG SKKFAKLIMA GNYEEALSVA KVQVEMGAQV LDINMDDGML DGPSAMTKFC
NFIASEPDIA KVPLCIDSSN FAVIEAGLKC CQGKCIVNSI SLKEGEEDFL EKARKIKKFG
AAVVVMAFDE EGQATETDVK VSVCTRAYHL LVEKVGFNPN DIIFDPNILT IGTGMEEHNL
YAINFIHATR VIKETLPGVR ISGGLSNLSF AFRGMDAIRE AMHGVFLYHA IKFGMDMGIV
NAGSLPVYDD IHKDLLQLCE DLIWNRDAEA TEKLLRYAQT HGKGGKKVIQ TDEWRNGSIE
ERLEYALVKG IEKHIVEDTE EARLNREKYP RPLNIIEGPL MNGMKVVGDL FGAGKMFLPQ
VIKSARVMKK AVGHLIPFME KEREEARVLN GSVEEEDPYQ GTIVLATVKG DVHDIGKNIV
GVVLGCNNFR VIDLGVMTPC DKILQAALDH KADIIGLSGL ITPSLDEMIF VAKEMERLAI
KIPLLIGGAT TSRTHTAVKI APRYSAPVIH VLDASKSVVV CSQLLDENLK DDYFEEILEE
YEDIRQDHYE SLKERKYLPL SQARKHSFHI DWLSEPHPVK PTFIGTQVFE DYNLQKLVDY
IDWKPFFDVW QLRGKYPNRG FPKIFNDKAV GEEARKVYED AQNMLSILIS RKKLRARGVV
GFWPAQSVQD DIHLYAEGAV PQAAEPIATF YGLRQQAEKD SSSTDPYHCL SDFVAPLHSG
VRDYLGLFAV ACFGVEELSK AYEDDGDDYS SIMVKALGDR LAEAFAEELH ERVRRELWAY
CGSEQLGVTD LRKLRYEGIR PAPGYPSQPD HTEKLTMWRL ANIEQATGIR LTESLAMAPA
SAVSGLYFSN VKSKYFAVGK ISKDQIEDYA LRKNMSVAEV EKWLGPILGY DTD


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