P13009 (METH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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:	b4019, JW3979

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	1227 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

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.
Catalytic activity	5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine.
Cofactor	Cobalamin. Binds 1 zinc ion per subunit.
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. Ref.7
Miscellaneous	L-homocysteine is bound via the zinc atom.
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	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	pteridine-containing compound metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from direct assay Ref.2. Source: EcoliWiki
Molecular function	cobalamin binding Inferred from direct assay. Source: EcoCyc homocysteine S-methyltransferase activity Inferred from direct assay Ref.7. Source: EcoCyc methionine synthase activity Inferred from direct assay Ref.7. Source: EcoCyc zinc ion binding Inferred from mutant phenotype Ref.10. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7

Chain

2 – 1227

1226

Methionine synthase

PRO_0000204532

Regions

Domain

2 – 325

324

Hcy-binding

Domain

356 – 617

262

Pterin-binding

Domain

650 – 744

95

B12-binding N-terminal

Domain

746 – 881

136

B12-binding

Domain

897 – 1227

331

AdoMet activation

Region

834 – 835

2

Cobalamin-binding

Region

1189 – 1190

2

S-adenosyl-L-methionine binding

Sites

Metal binding

247

1

Zinc

Metal binding

310

1

Zinc

Metal binding

311

1

Zinc

Metal binding

759

1

Cobalt (cobalamin axial ligand) Ref.13

Binding site

804

1

Cobalamin

Binding site

946

1

S-adenosyl-L-methionine

Binding site

1134

1

S-adenosyl-L-methionine; via carbonyl oxygen

Binding site

1138

1

Cobalamin; via carbonyl oxygen

Experimental info

Mutagenesis

310

1

C → A or S: Loss of zinc binding. Loss of catalytic activity. Ref.7

Mutagenesis

311

1

C → A or S: Loss of zinc binding. Loss of catalytic activity. Ref.7

Mutagenesis

757

1

D → E: Decreases activity by about 70%. Ref.9

Mutagenesis

757

1

D → N: Decreases activity by about 45%. Ref.9

Mutagenesis

759

1

H → G: Loss of catalytic activity. Ref.9

Mutagenesis

810

1

S → A: Decreases activity by about 40%. Ref.9

Sequence conflict

113

1

A → R Ref.1

Sequence conflict

113

1

A → R Ref.2

Sequence conflict

641

1

S → T Ref.1

Sequence conflict

641

1

S → T Ref.2

Sequence conflict

1079 – 1080

2

QH → HD in CAA34601. Ref.1

Sequence conflict

1195 – 1227

33

IQRDQ…GYDAD → TSARSG in CAA34601. Ref.1

Secondary structure

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1227

Helix Strand Turn

Details...

Helix

659 – 669

11

Helix

675 – 683

9

Beta strand

686 – 688

3

Helix

689 – 694

6

Helix

696 – 709

14

Helix

715 – 737

23

Beta strand

748 – 753

6

Helix

761 – 772

12

Beta strand

776 – 779

4

Helix

786 – 795

10

Beta strand

799 – 804

6

Helix

808 – 823

16

Beta strand

830 – 834

5

Helix

839 – 844

6

Helix

847 – 849

3

Beta strand

854 – 856

3

Beta strand

858 – 860

3

Helix

861 – 871

11

Turn

873 – 875

3

Helix

876 – 893

18

Helix

906 – 911

6

Beta strand

930 – 935

6

Helix

938 – 941

4

Helix

942 – 944

3

Helix

948 – 953

6

Helix

962 – 965

4

Turn

967 – 969

3

Helix

970 – 990

21

Beta strand

996 – 1007

12

Beta strand

1010 – 1016

7

Beta strand

1022 – 1027

6

Beta strand

1036 – 1038

3

Helix

1043 – 1046

4

Helix

1050 – 1052

3

Beta strand

1057 – 1065

9

Helix

1069 – 1078

10

Helix

1082 – 1109

28

Helix

1122 – 1126

5

Helix

1145 – 1147

3

Helix

1148 – 1154

7

Helix

1157 – 1161

5

Beta strand

1171 – 1182

12

Helix

1197 – 1207

11

Helix

1211 – 1218

8

Helix

1219 – 1221

3

Beta strand

1222 – 1224

3

Sequences

	Sequence		Length	Mass (Da)
	P13009 [UniParc]. Last modified January 23, 2007. Version 5. Checksum: 91F0CAA1E9127D9A	FASTA	1,227	135,997
	10 20 30 40 50 60 MSSKVEQLRA QLNERILVLD GGMGTMIQSY RLNEADFRGE RFADWPCDLK GNNDLLVLSK 70 80 90 100 110 120 PEVIAAIHNA YFEAGADIIE TNTFNSTTIA MADYQMESLS AEINFAAAKL ARACADEWTA 130 140 150 160 170 180 RTPEKPRYVA GVLGPTNRTA SISPDVNDPA FRNITFDGLV AAYRESTKAL VEGGADLILI 190 200 210 220 230 240 ETVFDTLNAK AAVFAVKTEF EALGVELPIM ISGTITDASG RTLSGQTTEA FYNSLRHAEA 250 260 270 280 290 300 LTFGLNCALG PDELRQYVQE LSRIAECYVT AHPNAGLPNA FGEYDLDADT MAKQIREWAQ 310 320 330 340 350 360 AGFLNIVGGC CGTTPQHIAA MSRAVEGLAP RKLPEIPVAC RLSGLEPLNI GEDSLFVNVG 370 380 390 400 410 420 ERTNVTGSAK FKRLIKEEKY SEALDVARQQ VENGAQIIDI NMDEGMLDAE AAMVRFLNLI 430 440 450 460 470 480 AGEPDIARVP IMIDSSKWDV IEKGLKCIQG KGIVNSISMK EGVDAFIHHA KLLRRYGAAV 490 500 510 520 530 540 VVMAFDEQGQ ADTRARKIEI CRRAYKILTE EVGFPPEDII FDPNIFAVAT GIEEHNNYAQ 550 560 570 580 590 600 DFIGACEDIK RELPHALISG GVSNVSFSFR GNDPVREAIH AVFLYYAIRN GMDMGIVNAG 610 620 630 640 650 660 QLAIYDDLPA ELRDAVEDVI LNRRDDGTER LLELAEKYRG SKTDDTANAQ QAEWRSWEVN 670 680 690 700 710 720 KRLEYSLVKG ITEFIEQDTE EARQQATRPI EVIEGPLMDG MNVVGDLFGE GKMFLPQVVK 730 740 750 760 770 780 SARVMKQAVA YLEPFIEASK EQGKTNGKMV IATVKGDVHD IGKNIVGVVL QCNNYEIVDL 790 800 810 820 830 840 GVMVPAEKIL RTAKEVNADL IGLSGLITPS LDEMVNVAKE MERQGFTIPL LIGGATTSKA 850 860 870 880 890 900 HTAVKIEQNY SGPTVYVQNA SRTVGVVAAL LSDTQRDDFV ARTRKEYETV RIQHGRKKPR 910 920 930 940 950 960 TPPVTLEAAR DNDFAFDWQA YTPPVAHRLG VQEVEASIET LRNYIDWTPF FMTWSLAGKY 970 980 990 1000 1010 1020 PRILEDEVVG VEAQRLFKDA NDMLDKLSAE KTLNPRGVVG LFPANRVGDD IEIYRDETRT 1030 1040 1050 1060 1070 1080 HVINVSHHLR QQTEKTGFAN YCLADFVAPK LSGKADYIGA FAVTGGLEED ALADAFEAQH 1090 1100 1110 1120 1130 1140 DDYNKIMVKA LADRLAEAFA EYLHERVRKV YWGYAPNENL SNEELIRENY QGIRPAPGYP 1150 1160 1170 1180 1190 1200 ACPEHTEKAT IWELLEVEKH TGMKLTESFA MWPGASVSGW YFSHPDSKYY AVAQIQRDQV 1210 1220 EDYARRKGMS VTEVERWLAP NLGYDAD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2." Old I.G., Margarita D., Glass R.E., Saint-Girons I. Gene 87:15-21(1990) [PubMed: 2185137] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Cloning and sequence analysis of the Escherichia coli metH gene encoding cobalamin-dependent methionine synthase and isolation of a tryptic fragment containing the cobalamin-binding domain." Banerjee R.V., Johnston N.L., Sobeski J.K., Datta P., Matthews R.G. J. Biol. Chem. 264:13888-13895(1989) [PubMed: 2668277] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: K12.
[3]	"Electrospray mass spectrometric analysis of the domains of a large enzyme: observation of the occupied cobalamin-binding domain and redefinition of the carboxyl terminus of methionine synthase." Drummond J.T., Loo R.R., Matthews R.G. Biochemistry 32:9282-9289(1993) [PubMed: 8369296] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed: 8265357] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine." Goulding C.W., Postigo D., Matthews R.G. Biochemistry 36:8082-8091(1997) [PubMed: 9201956] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-7, CHARACTERIZATION, DOMAIN, MUTAGENESIS OF CYS-310 AND CYS-311. Strain: K12.
[8]	"Crystallization and preliminary X-ray diffraction studies of the cobalamin-binding domain of methionine synthase from Escherichia coli." Luschinsky C.L., Drummond J.T., Matthews R.G., Ludwig M.L. J. Mol. Biol. 225:557-560(1992) [PubMed: 1593636] [Abstract] Cited for: CRYSTALLIZATION.
[9]	"Mutations in the B12-binding region of methionine synthase: how the protein controls methylcobalamin reactivity." Jarrett J.T., Amaratunga M., Drennan C.L., Scholten J.D., Sands R.H., Ludwig M.L., Matthews R.G. Biochemistry 35:2464-2475(1996) [PubMed: 8652590] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF ASP-757; HIS-759 AND SER-810. Strain: K12.
[10]	"Cobalamin-dependent methionine synthase from Escherichia coli: involvement of zinc in homocysteine activation." Goulding C.W., Matthews R.G. Biochemistry 36:15749-15757(1997) [PubMed: 9398304] [Abstract] Cited for: ZINC BINDING SITES. Strain: K12.
[11]	"Characterization of the zinc sites in cobalamin-independent and cobalamin-dependent methionine synthase using zinc and selenium X-ray absorption spectroscopy." Peariso K., Zhou Z.S., Smith A.E., Matthews R.G., Penner-Hahn J.E. Biochemistry 40:987-993(2001) [PubMed: 11170420] [Abstract] Cited for: ZINC BINDING SITES, ROLE OF ZINC IN SUBSTRATE BINDING. Strain: K12.
[12]	"Cobalamin-dependent methyltransferases." Matthews R.G. Acc. Chem. Res. 34:681-689(2001) [PubMed: 11513576] [Abstract] Cited for: REVIEW.
[13]	"How a protein binds B12: a 3.0 A X-ray structure of B12-binding domains of methionine synthase." Drennan C.L., Huang S., Drummond J.T., Matthews R.G., Ludwig M.L. Science 266:1669-1674(1994) [PubMed: 7992050] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 651-896 IN COMPLEX WITH COBALAMIN.
[14]	"The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12." Dixon M.M., Huang S., Matthews R.G., Ludwig M.L. Structure 4:1263-1275(1996) [PubMed: 8939751] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 897-1227 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE. Strain: K12.
[15]	"Domain alternation switches B(12)-dependent methionine synthase to the activation conformation." Bandarian V., Pattridge K.A., Lennon B.W., Huddler D.P., Matthews R.G., Ludwig M.L. Nat. Struct. Biol. 9:53-56(2002) [PubMed: 11731805] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 651-1227 OF WILD-TYPE AND MUTANT GLY-759 IN COMPLEX WITH COBALAMIN. Strain: K12.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X16584 Genomic DNA. Translation: CAA34601.1.
J04975 Unassigned DNA. Translation: AAA02995.1.
U00006 Genomic DNA. Translation: AAC43113.1.
U00096 Genomic DNA. Translation: AAC76989.1.
AP009048 Genomic DNA. Translation: BAE78021.1.

PIR

XYECMH. B65209.

RefSeq

NP_418443.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BMT	X-ray	3.00	A/B	651-896	[»]
1K7Y	X-ray	3.00	A	651-1227	[»]
1K98	X-ray	3.75	A	651-1227	[»]
1MSK	X-ray	1.80	A	897-1227	[»]
3BUL	X-ray	2.30	A	649-1227	[»]
3IV9	X-ray	3.25	A	649-1227	[»]
3IVA	X-ray	2.70	A	649-1227	[»]

ProteinModelPortal

P13009.

SMR

P13009. Positions 356-1227.

ModBase

Search...

Protein-protein interaction databases

IntAct

P13009. 13 interactions.

2D gel databases

SWISS-2DPAGE

P13009.

ECO2DBASE

C137.0. 6TH EDITION.

Proteomic databases

PRIDE

P13009.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000002831; EBESCP00000002831; EBESCG00000002309.
EBESCT00000018146; EBESCP00000017437; EBESCG00000017201.

GeneID

948522.

GenomeReviews

Gene locus JW3979 in contig AP009048_GR.
Gene locus b4019 in contig U00096_GR.

KEGG

ecj:JW3979.
eco:b4019.

PATRIC

32123567. VBIEscCol129921_4132.

Organism-specific databases

EchoBASE

EB0582.

EcoGene

EG10587. metH.

Phylogenomic databases

eggNOG

COG1410.

GeneTree

EBGT00050000010605.

HOGENOM

HBG289648.

OMA

YVTDASR.

PhylomeDB

P13009.

ProtClustDB

PRK09490.

Enzyme and pathway databases

BioCyc

EcoCyc:HOMOCYSMETB12-MONOMER.
MetaCyc:HOMOCYSMETB12-MONOMER.

Gene expression databases

Genevestigator

P13009.

Family and domain databases

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]

Gene3D

G3DSA:3.40.50.280. B12_bd. 1 hit.
G3DSA:3.20.20.20. Dhdropt_synth. 1 hit.
G3DSA:3.10.196.10. Met_synth_B12. 1 hit.
G3DSA:1.10.1240.10. Met_synth_B12_bd. 1 hit.
G3DSA:3.20.20.330. S_methyl_trans. 1 hit.

KO

K00548.

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_ECOLI

Accession

Primary (citable) accession number: P13009
Secondary accession number(s): Q2M6T5

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 132 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program