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Protein

Methionine synthase

Gene

metH

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed-Annotation score: 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: L-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 (metH)
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)DescriptionActionsGraphical viewLength
Metal bindingi228ZincPROSITE-ProRule annotation1
Metal bindingi294ZincPROSITE-ProRule annotation1
Metal bindingi295ZincPROSITE-ProRule annotation1
Metal bindingi737Cobalt (cobalamin axial ligand)By similarity1
Binding sitei782CobalaminBy similarity1
Binding sitei945S-adenosyl-L-methionineBy similarity1
Binding sitei1138S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1
Binding sitei1142Cobalamin; via carbonyl oxygenBy similarity1

GO - Molecular functioni

GO - Biological processi

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
Methionine synthase, vitamin-B12 dependent
Short name:
MS
Gene namesi
Name:metH
Ordered Locus Names:slr0212
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesMerismopediaceaeSynechocystis
Proteomesi
  • UP000001425 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002045371 – 1195Methionine synthaseAdd BLAST1195

Proteomic databases

PRIDEiQ55786.

Structurei

3D structure databases

ProteinModelPortaliQ55786.
SMRiQ55786.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 309Hcy-bindingPROSITE-ProRule annotationAdd BLAST309
Domaini340 – 599Pterin-bindingPROSITE-ProRule annotationAdd BLAST260
Domaini629 – 722B12-binding N-terminalPROSITE-ProRule annotationAdd BLAST94
Domaini724 – 859B12-bindingPROSITE-ProRule annotationAdd BLAST136
Domaini896 – 1195AdoMet activationPROSITE-ProRule annotationAdd BLAST300

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni812 – 813Cobalamin-bindingBy similarity2
Regioni1192 – 1193S-adenosyl-L-methionine bindingBy similarity2

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 B12-binding N-terminal 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

HOGENOMiHOG000251408.
InParanoidiQ55786.
KOiK00548.
OMAiDYNSIMV.
PhylomeDBiQ55786.

Family and domain databases

CDDicd02069. methionine_synthase_B12_BD. 1 hit.
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.
IPR003726. HCY_dom.
IPR033706. Met_synthase_B12-bd.
IPR011822. MetH.
IPR000489. Pterin-binding_dom.
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.

Q55786-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKSAFLDRIH SPDRPVLVFD GAMGTNLQVQ NLTAADFGGA EYEGCNEYLV
60 70 80 90 100
HTKPEAVATV HRAFYEAGAD VVETDTFGGT PLVLAEYDLA DQSYYLNKAA
110 120 130 140 150
AELAKAVAAE FSTPEKPRFV AGSMGPGTKL PTLGHVDYDS LKDAYVVQVR
160 170 180 190 200
GLYDGGVDLL LVETCQDVLQ IKAALNAIEQ VFAEKGDRLP LMVSVTMETM
210 220 230 240 250
GTMLVGTEMA AALAILEPYP IDILGLNCAT GPDLMKEHVK YLSEHSPFVV
260 270 280 290 300
SCIPNAGLPE NVGGQAFYRL TPMELQMSLM HFIEDLGVQV IGGCCGTRPD
310 320 330 340 350
HIKALADIAK DLQPKQRQPH YEPSAASIYS TQTYAQENSF LIIGERLNAS
360 370 380 390 400
GSKKCRDLLN AEDWDSLVSL AKSQVKEGAQ ILDVNVDYVG RDGVRDMKEL
410 420 430 440 450
ASRLVNNVTL PLMLDSTEWQ KMEAGLKVAG GKCILNSTNY EDGEERFYKV
460 470 480 490 500
LEIAKEYGAG IVIGTIDEDG MGRTADKKFE IAKRAYEAAI AFGIPATEIF
510 520 530 540 550
FDPLALPIST GIEEDRENGK ATVDAIRRIR QELPDCHILL GVSNVSFGLN
560 570 580 590 600
PAARQVLNSI FLHECMQVGM DAAIVSANKI LPLAKIDPEQ QQVCLDLIYD
610 620 630 640 650
RREFEGERCT YDPLTKLTTL FEGKTTKRDK SGDANLPVEE RLKRHIIDGE
660 670 680 690 700
RLGLEEALNE ALKLYAPLDI INIYLLDGMK VVGELFGSGQ MQLPFVLQSA
710 720 730 740 750
QTMKAAVAFL EPHMDKDDSA DNAKGTFLIA TVKGDVHDIG KNLVDIILSN
760 770 780 790 800
NGYRVVNLGI KQPVENIIEA YKKHRPDCIA MSGLLVKSTA FMKENLEVFN
810 820 830 840 850
QEGITVPVIL GGAALTPKFV HQDCQNTYKG QVIYGKDAFA DLHFMDKLMP
860 870 880 890 900
AKNSHNWDDF QGFLGEYATE NGHNVTTDDG AKTNFGIEEE KLIDASEQSR
910 920 930 940 950
EPEVIDTVRS EAVDPDLERP VPPFWGTKIL QSSDISLDEV FPLLDLQALF
960 970 980 990 1000
VGQWQFRKPR EQSREEYEQF LAEKVHPILA EWKGKVMAEN LLHPTVVYGY
1010 1020 1030 1040 1050
FPCQSQGNTL LIYDPELVSQ NNGQIPPDAT AIAKFEFPRQ KSGRRLCIAD
1060 1070 1080 1090 1100
FFASKESGIT DVFPLQAVTV GEIATEYARK LFAGDNYTDY LYFHGMAVQM
1110 1120 1130 1140 1150
AEALAEWTHQ RIRQELGFGH LDPDNIRDLL QQRYQGSRYS FGYPACPNMQ
1160 1170 1180 1190
DQYTQLELLQ TERIGLYMDE SEQVYPEQST TAIISYHPAA KYFSA
Length:1,195
Mass (Da):132,540
Last modified:November 1, 1996 - v1
Checksum:i1D9635B1B1DDB583
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA10438.1.
PIRiS76592.

Genome annotation databases

EnsemblBacteriaiBAA10438; BAA10438; BAA10438.
KEGGisyn:slr0212.
PATRICi23842418. VBISynSp132158_2749.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA10438.1.
PIRiS76592.

3D structure databases

ProteinModelPortaliQ55786.
SMRiQ55786.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ55786.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA10438; BAA10438; BAA10438.
KEGGisyn:slr0212.
PATRICi23842418. VBISynSp132158_2749.

Phylogenomic databases

HOGENOMiHOG000251408.
InParanoidiQ55786.
KOiK00548.
OMAiDYNSIMV.
PhylomeDBiQ55786.

Enzyme and pathway databases

UniPathwayiUPA00051; UER00081.

Family and domain databases

CDDicd02069. methionine_synthase_B12_BD. 1 hit.
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.
IPR003726. HCY_dom.
IPR033706. Met_synthase_B12-bd.
IPR011822. MetH.
IPR000489. Pterin-binding_dom.
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...

Entry informationi

Entry nameiMETH_SYNY3
AccessioniPrimary (citable) accession number: Q55786
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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
  3. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

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 one 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.