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Q87L95

- METH_VIBPA

UniProt

Q87L95 - METH_VIBPA

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Protein

Methionine synthase

Gene

metH

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
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 bindingi248 – 2481ZincPROSITE-ProRule annotation
Metal bindingi311 – 3111ZincPROSITE-ProRule annotation
Metal bindingi312 – 3121ZincPROSITE-ProRule annotation
Metal bindingi760 – 7601Cobalt (cobalamin axial ligand)By similarity
Binding sitei805 – 8051CobalaminBy similarity
Binding sitei948 – 9481S-adenosyl-L-methionineBy similarity
Binding sitei1136 – 11361S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei1140 – 11401Cobalamin; via carbonyl oxygenBy similarity

GO - Molecular functioni

  1. cobalamin binding Source: UniProtKB-KW
  2. methionine synthase activity Source: UniProtKB-EC
  3. S-adenosylmethionine-homocysteine S-methyltransferase activity Source: InterPro
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. 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

BioCyciVPAR223926:GHK4-2806-MONOMER.
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:VP2717
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493: Chromosome 1

Subcellular locationi

GO - Cellular componenti

  1. intracellular Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12261226Methionine synthasePRO_0000204541Add
BLAST

Proteomic databases

PRIDEiQ87L95.

Interactioni

Protein-protein interaction databases

STRINGi223926.VP2717.

Structurei

3D structure databases

ProteinModelPortaliQ87L95.
SMRiQ87L95. Positions 654-1224.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 326321Hcy-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini357 – 618262Pterin-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini651 – 74595B12-binding N-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini747 – 882136B12-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini898 – 1226329AdoMet activationPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni835 – 8362Cobalamin-bindingBy similarity
Regioni1191 – 11922S-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.
KOiK00548.
OMAiLTEHYAM.
OrthoDBiEOG6091CH.

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.

Q87L95-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGSKVRQQIE AQLKQRILLI DGGMGTMIQG YKLEEQDYRG ERFANWHCDL
60 70 80 90 100
KGNNDLLVLS QPQLIKEIHS AYLEAGADIL ETNTFNATTI AMADYEMESL
110 120 130 140 150
SEEINFAAAK LAREVADEWT AKTPDKPRYV AGVLGPTNRT CSISPDVNDP
160 170 180 190 200
GYRNVSFDEL VEAYSESTRA LIRGGADLIL IETIFDTLNA KACAFAVDSV
210 220 230 240 250
FEELGVALPV MISGTITDAS GRTLSGQTTE AFYNSLRHVR PLSFGLNCAL
260 270 280 290 300
GPDELRPYVE ELSRISESFV SAHPNAGLPN AFGEYDLSPE DMAEHVKEWA
310 320 330 340 350
SSGFLNLIGG CCGTTPEHIR QMAQAVEGVT PRALPDLPVA CRLSGLEPLT
360 370 380 390 400
IEKETLFINV GERTNVTGSA RFKRLIKEEQ YDEALEVARQ QVENGAQIID
410 420 430 440 450
INMDEGMLDA QACMVRFLNL CASEPEISKV PIMVDSSKWE VIEAGLKCIQ
460 470 480 490 500
GKGIVNSISL KEGKEKFVEQ AKLIRRYGAA VIVMAFDEVG QAETRTRKLE
510 520 530 540 550
ICTNAYRILV DEVGFPPEDI IFDPNIFAVA TGIDEHNNYA VDFIEAVADI
560 570 580 590 600
KRDLPHAMIS GGVSNVSFSF RGNNYVREAI HAVFLYHCFK NGMDMGIVNA
610 620 630 640 650
GQLEIYDNVP EKLREAVEDV VLNRRDDATE RLLDIAAEYA DKGVGKEEDA
660 670 680 690 700
SALEWRTWPV AKRLEHALVK GITEFIVADT EEARVNAVKP LEVIEGPLMD
710 720 730 740 750
GMNVVGDLFG EGKMFLPQVV KSARVMKQAV AHLEPFINAE KQSGSSNGKI
760 770 780 790 800
LLATVKGDVH DIGKNIVGVV LQCNNYEIID LGVMVPCEKI LKVAIEENVD
810 820 830 840 850
IIGLSGLITP SLDEMVHVAK EMERLNFDLP LLIGGATTSK AHTAVKIEQN
860 870 880 890 900
YKNPVVYVNN ASRAVGVCSS LLSDERRPAF IEKLDADYER VRDQHNRKKP
910 920 930 940 950
RTKPVTLEQA RANKVAIDWD AYTPPVPAKP GLHIFDDFDV ATLRKYIDWT
960 970 980 990 1000
PFFMTWSLVG KYPTIFKHEE VGEEAQRLFH DANELLDRVE REGLLKARGI
1010 1020 1030 1040 1050
CGLFPAASVG DDIEVYTDES RTEVAKVLRN LRQQTEKPKG FNYCLSDYIA
1060 1070 1080 1090 1100
PKESGKQDWV GAFAVTGGIG ERELADEYKA QGDDYNAIMI QAVADRLAEA
1110 1120 1130 1140 1150
FAEYLHERVR KEIWGYAADE NLSNDELIRE KYQGIRPAPG YPACPEHTEK
1160 1170 1180 1190 1200
GPLWELLNVE ENIGMSLTTS YAMYPGASVS GWYFSHPDSR YFAIAQIQDD
1210 1220
QLESYADRKG WDRIEAEKWL GPNING
Length:1,226
Mass (Da):136,218
Last modified:June 1, 2003 - v1
Checksum:i2F7A3269FB7C20A9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC60980.1.
RefSeqiNP_799096.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC60980; BAC60980; BAC60980.
GeneIDi1190262.
KEGGivpa:VP2717.
PATRICi20143630. VBIVibPar50997_2612.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC60980.1 .
RefSeqi NP_799096.1. NC_004603.1.

3D structure databases

ProteinModelPortali Q87L95.
SMRi Q87L95. Positions 654-1224.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 223926.VP2717.

Proteomic databases

PRIDEi Q87L95.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAC60980 ; BAC60980 ; BAC60980 .
GeneIDi 1190262.
KEGGi vpa:VP2717.
PATRICi 20143630. VBIVibPar50997_2612.

Phylogenomic databases

eggNOGi COG1410.
HOGENOMi HOG000251409.
KOi K00548.
OMAi LTEHYAM.
OrthoDBi EOG6091CH.

Enzyme and pathway databases

UniPathwayi UPA00051 ; UER00081 .
BioCyci VPAR223926:GHK4-2806-MONOMER.

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. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiMETH_VIBPA
AccessioniPrimary (citable) accession number: Q87L95
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: June 1, 2003
Last modified: November 26, 2014
This is version 80 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

External Data

Dasty 3