Methionine synthase - Vibrio vulnificus (strain CMCP6)

Preferred order of sections

Names and origin

Protein names

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 names

Name:	metH
Ordered Locus Names:	VV1_1423

Organism

Vibrio vulnificus (strain CMCP6) [Complete proteome] [HAMAP]

Taxonomic identifier

216895 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio ›

Protein attributes

Sequence length	1226 AA.
Sequence status	Complete.
Protein existence	Inferred 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	Cobalamin 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.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Methionine biosynthesis
Domain	Repeat
Ligand	Cobalamin Cobalt Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Methyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	pteridine-containing compound metabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular_function	cobalamin binding Inferred from electronic annotation. Source: UniProtKB-KW homocysteine S-methyltransferase activity Inferred from electronic annotation. Source: InterPro methionine synthase activity Inferred from electronic annotation. Source: EC zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1226

1226

Methionine synthase

PRO_0000204542

Regions

Domain

6 – 326

321

Hcy-binding

Domain

357 – 618

262

Pterin-binding

Domain

651 – 745

95

B12-binding N-terminal

Domain

747 – 882

136

B12-binding

Domain

898 – 1226

329

AdoMet activation

Region

835 – 836

2

Cobalamin-binding By similarity

Region

1191 – 1192

2

S-adenosyl-L-methionine binding By similarity

Sites

Metal binding

248

1

Zinc By similarity

Metal binding

311

1

Zinc By similarity

Metal binding

312

1

Zinc By similarity

Metal binding

760

1

Cobalt (cobalamin axial ligand) By similarity

Binding site

805

1

Cobalamin By similarity

Binding site

948

1

S-adenosyl-L-methionine By similarity

Binding site

1136

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

1140

1

Cobalamin; via carbonyl oxygen By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q8DCJ7 [UniParc].

Last modified March 1, 2003. Version 1.
Checksum: 51E8263EBD605A19
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FASTA

1,226

136,241

        10         20         30         40         50         60 
MGSQIRAQIE AQLKQRILLI DGGMGTMIQG YKLQEQDYRG ERFADWHSDL KGNNDLLVLT 

        70         80         90        100        110        120 
QPQLIKEIHH AYLEAGADIL ETNTFNATTI AMADYDMESL SEEINFAAAR LAREAADEWT 

       130        140        150        160        170        180 
AQNPAKPRYV AGVLGPTNRT CSISPDVNDP GYRNVSFDEL VEAYSESTRA LIRGGSDLIL 

       190        200        210        220        230        240 
IETIFDTLNA KACAFAVDSV FEELGFALPV MISGTITDAS GRTLSGQTTE AFYNSLRHVR 

       250        260        270        280        290        300 
PISFGLNCAL GPDELRPYVE ELSRISETFV STHPNAGLPN AFGEYDLSPE EMAEHVKEWA 

       310        320        330        340        350        360 
QSGFLNLIGG CCGTTPEHIR HMAMAVEGVS PRVLPEIPVA CRLSGLEPLT IAKDTLFVNV 

       370        380        390        400        410        420 
GERTNVTGSA RFKRLIKEEL YDEALDVARE QVENGAQIID INMDEGMLDA EACMVRFLNL 

       430        440        450        460        470        480 
CASEPEISKV PIMVDSSKWE VIEAGLKCIQ GKGIVNSISL KEGKEKFVEQ AKLIRRYGAA 

       490        500        510        520        530        540 
VIVMAFDEVG QADTRERKLE ICTKAYRILV DEVGFPPEDV IFDPNIFAVA TGIDEHNNYA 

       550        560        570        580        590        600 
VDFIEAVADI KRDLPHAMIS GGVSNVSFSF RGNNYVREAI HAVFLYHCFK NGMDMGIVNA 

       610        620        630        640        650        660 
GQLEIYDNVP EKLREAVEDV VLNRRDDATE RLLEIAEEYR ENAVGKQEDA SALEWRTWSV 

       670        680        690        700        710        720 
EKRLEHALVK GITEFIVEDT EEARLNASKP LEVIEGPLMD GMNVVGDLFG EGKMFLPQVV 

       730        740        750        760        770        780 
KSARVMKQAV AHLEPFINAS KQAGSSNGKI LLATVKGDVH DIGKNIVGVV LQCNNYEIID 

       790        800        810        820        830        840 
LGVMVPCEQI LKVAKEQQVD IIGLSGLITP SLDEMVHVAK EMERLGFDLP LLIGGATTSK 

       850        860        870        880        890        900 
AHTAVKIEQN YSHPVVYVNN ASRAVGVCTS LLSDELRPAF VERLQADYEL VRDQHNRKKP 

       910        920        930        940        950        960 
RTKPVTLEAA RANKVAIDWQ SYTPPAPSQP GVHVFDDFDV ATLRQYIDWT PFFLTWSLVG 

       970        980        990       1000       1010       1020 
KYPTIFEHEE VGEEAKRLFG DANEWLDRIE QEGLLKARGM CGLFPAASVG DDIEVYTDES 

      1030       1040       1050       1060       1070       1080 
RTHVAKVLHN LRQQTEKPKG ANYCLSDYVA PKESGKKDWI GAFAVTGGVN ERELADQFKA 

      1090       1100       1110       1120       1130       1140 
QGDDYNAIMI QAVADRLAEA FAEYLHERVR KEIWGYAADE NLSNEELIRE KYQGIRPAPG 

      1150       1160       1170       1180       1190       1200 
YPACPEHTEK GPLWELLNVE ETIGMSLTSS YAMWPGASVS GWYFSHPDSR YFAIAQIQQD 

      1210       1220 
QVESYAERKG WDLLEAEKWL GPNING

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References

[1]	"Complete genome sequence of Vibrio vulnificus CMCP6." Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E. Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CMCP6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE016795 Genomic DNA. Translation: AAO09863.1.
RefSeq	NP_760336.1. NC_004459.3.
3D structure databases
ProteinModelPortal	Q8DCJ7.
SMR	Q8DCJ7. Positions 654-1224.
ModBase	Search...
Protein-protein interaction databases
STRING	216895.VV1_1423.
Proteomic databases
PRIDE	Q8DCJ7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAO09863; AAO09863; VV1_1423.
GeneID	1178338.
KEGG	vvu:VV1_1423.
PATRIC	20159626. VBIVibVul94426_1325.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1410.
HOGENOM	HOG000251409.
KO	K00548.
OMA	VRKEFWG.
ProtClustDB	PRK09490.
Enzyme and pathway databases
UniPathway	UPA00051; UER00081.
Family and domain databases
Gene3D	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.
InterPro	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]
PANTHER	PTHR21091:SF9. PTHR21091:SF9. 1 hit.
Pfam	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]
PIRSF	PIRSF000381. MetH. 1 hit.
SMART	SM01018. B12-binding_2. 1 hit. [Graphical view]
SUPFAM	SSF52242. Cbl-bd. 1 hit. SSF51717. DHP_synth_like. 1 hit. SSF56507. Met_synth_B12. 1 hit. SSF47644. Met_synth_Cbl-bd. 1 hit. SSF82282. S_methyl_trans. 1 hit.
TIGRFAMs	TIGR02082. metH. 1 hit.
PROSITE	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]
ProtoNet	Search...

Entry information

Entry name

METH_VIBVU

Accession

Primary (citable) accession number: Q8DCJ7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	March 1, 2003
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents