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metH:On One Page

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Standard Name

metH

Gene Synonym(s)

ECK4011, b4019, JW3979[1]

Product Desc.

Methionine synthase, cobalamin-dependent; 5-methyltetrahydrofolate-homocysteine methyltransferase; binds Zn(II)[2]

Product Synonyms(s)

homocysteine-N5-methyltetrahydrofolate transmethylase, B12-dependent[1], B4019[3][1], MetH[3][1]

Function from GO

Cellular Component

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): metH[3], OP00055

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(metH)    Textpresso(metH)

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

metH

Mnemonic

Methionine

Synonyms

ECK4011, b4019, JW3979[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

90.99 minutes 

MG1655: 4221851..4225534
gbrowse_img.php?coord=4221851..4225534&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4202759..4206442
gbrowse_img.php?coord=4202759..4206442&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4227418..4231101
gbrowse_img.php?coord=4227418..4231101&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4321547..4325230
gbrowse_img.php?coord=4321547..4325230&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 4111531..4115214
gbrowse_img.php?coord=4111531..4115214&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔmetH (Keio:JW3979)

deletion

deletion

PMID:16738554

Shigen
CGSC10862[4]

metHC310A,S

C310A,S

Loss of zinc binding. Loss of catalytic activity

seeded from UniProt:P13009

metHC311A,S

C311A,S

Loss of zinc binding. Loss of catalytic activity

seeded from UniProt:P13009

metHD757E

D757E

Decreases activity by about 70%

seeded from UniProt:P13009

metHD757N

D757N

Decreases activity by about 45%

seeded from UniProt:P13009

metHH759G

H759G

Loss of catalytic activity

seeded from UniProt:P13009

metHS810A

S810A

Decreases activity by about 40%

seeded from UniProt:P13009

metH156

PMID:4579870

CGSC:9164

ΔmetH786::kan

PMID:16738554

CGSC:101834


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW3979

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCAGCAAAGTGGAACAACT

Primer 2:CCGTCCGCGTCATACCCCAGATT

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[4]

est. P1 cotransduction: 35% [5]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[4]

est. P1 cotransduction: 51% [5]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10587

EchoBASE (EcoliWiki Page)

EchoBASE:EB0582

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4019

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4976

EcoGene (EcoliWiki Page)

EcoGene:EG10587

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:METH

CGSC (EcoliWiki Page)

CGSC:509

ASAP (EcoliWikiPage)

ASAP:ABE-0013140


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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

MetH

Synonyms

homocysteine-N5-methyltetrahydrofolate transmethylase, B12-dependent[1], B4019[3][1], MetH[3][1]

Product description

Methionine synthase, cobalamin-dependent; 5-methyltetrahydrofolate-homocysteine methyltransferase; binds Zn(II)[2]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0004156

dihydropteroate synthase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000489

F

Seeded from EcoCyc [6]

complete

GO:0005622

intracellular

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004223

C

Seeded from EcoCyc [6]

complete

GO:0008168

methyltransferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc [6]

complete

GO:0008270

zinc ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc [6]

complete

GO:0008652

amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0028

P

Seeded from EcoCyc [6]

complete

GO:0008705

methionine synthase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR003759
InterPro:IPR004223
InterPro:IPR011822
EC:2.1.1.13

F

Seeded from EcoCyc [6]

complete

GO:0008898

homocysteine S-methyltransferase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003726

F

Seeded from EcoCyc [6]

complete

GO:0009086

methionine biosynthetic process

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003759
InterPro:IPR004223
InterPro:IPR011822
SP_KW:KW-0486

P

Seeded from EcoCyc [6]

complete

GO:0009396

folic acid and derivative biosynthetic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000489

P

Seeded from EcoCyc [6]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [6]

complete

GO:0031419

cobalamin binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003759
InterPro:IPR006158
InterPro:IPR011822
SP_KW:KW-0846

F

Seeded from EcoCyc [6]

complete

GO:0044237

cellular metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011005

P

Seeded from EcoCyc [6]

complete

GO:0046872

metal ion binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003759
InterPro:IPR006158
SP_KW:KW-0479

F

Seeded from EcoCyc [6]

complete

GO:0050897

cobalt ion binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR011822
SP_KW:KW-0170

F

Seeded from EcoCyc [6]

complete

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

required fields missing

GO:0006556

S-adenosylmethionine biosynthetic process

P

Seeded from EcoCyc 11.1[7].

required fields missing

GO:0009257

10-formyltetrahydrofolate biosynthetic process

P

Seeded from EcoCyc 11.1[7].

required fields missing

GO:0009236

cobalamin biosynthetic process

P

Seeded from EcoCyc 11.1[7].

required fields missing

GO:0005737

cytoplasm

PMID:9250984

IDA: Inferred from Direct Assay

C

complete

GO:0005737

cytoplasm

PMID:2668277

IDA: Inferred from Direct Assay

C

complete

GO:0008705

methionine synthase activity

PMID:10978155

IDA: Inferred from Direct Assay

F

complete

GO:0008168

methyltransferase activity

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

F

complete

GO:0008898

homocysteine S-methyltransferase activity

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

F

complete

GO:0009257

10-formyltetrahydrofolate biosynthetic process

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

P

complete

GO:0008705

methionine synthase activity

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

F

complete

GO:0008652

amino acid biosynthetic process

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

P

complete

GO:0009086

methionine biosynthetic process

Taylor and Weissbach (1971)[8]

IDA: Inferred from Direct Assay

P

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

gltB

PMID:16606699

Experiment(s):EBI-1147304

Protein

dnaE

PMID:16606699

Experiment(s):EBI-1147304

Protein

ilvC

PMID:16606699

Experiment(s):EBI-1147304

Protein

bglX

PMID:16606699

Experiment(s):EBI-1147304

Small Molecule

Cobalamin

PMID:9201956


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MSSKVEQLRA QLNERILVLD GGMGTMIQSY RLNEADFRGE RFADWPCDLK GNNDLLVLSK
PEVIAAIHNA YFEAGADIIE TNTFNSTTIA MADYQMESLS AEINFAAAKL ARACADEWTA
RTPEKPRYVA GVLGPTNRTA SISPDVNDPA FRNITFDGLV AAYRESTKAL VEGGADLILI
ETVFDTLNAK AAVFAVKTEF EALGVELPIM ISGTITDASG RTLSGQTTEA FYNSLRHAEA
LTFGLNCALG PDELRQYVQE LSRIAECYVT AHPNAGLPNA FGEYDLDADT MAKQIREWAQ
AGFLNIVGGC CGTTPQHIAA MSRAVEGLAP RKLPEIPVAC RLSGLEPLNI GEDSLFVNVG
ERTNVTGSAK FKRLIKEEKY SEALDVARQQ VENGAQIIDI NMDEGMLDAE AAMVRFLNLI
AGEPDIARVP IMIDSSKWDV IEKGLKCIQG KGIVNSISMK EGVDAFIHHA KLLRRYGAAV
VVMAFDEQGQ ADTRARKIEI CRRAYKILTE EVGFPPEDII FDPNIFAVAT GIEEHNNYAQ
DFIGACEDIK RELPHALISG GVSNVSFSFR GNDPVREAIH AVFLYYAIRN GMDMGIVNAG
QLAIYDDLPA ELRDAVEDVI LNRRDDGTER LLELAEKYRG SKTDDTANAQ QAEWRSWEVN
KRLEYSLVKG ITEFIEQDTE EARQQATRPI EVIEGPLMDG MNVVGDLFGE GKMFLPQVVK
SARVMKQAVA YLEPFIEASK EQGKTNGKMV IATVKGDVHD IGKNIVGVVL QCNNYEIVDL
GVMVPAEKIL RTAKEVNADL IGLSGLITPS LDEMVNVAKE MERQGFTIPL LIGGATTSKA
HTAVKIEQNY SGPTVYVQNA SRTVGVVAAL LSDTQRDDFV ARTRKEYETV RIQHGRKKPR
TPPVTLEAAR DNDFAFDWQA YTPPVAHRLG VQEVEASIET LRNYIDWTPF FMTWSLAGKY
PRILEDEVVG VEAQRLFKDA NDMLDKLSAE KTLNPRGVVG LFPANRVGDD IEIYRDETRT
HVINVSHHLR QQTEKTGFAN YCLADFVAPK LSGKADYIGA FAVTGGLEED ALADAFEAQH
DDYNKIMVKA LADRLAEAFA EYLHERVRKV YWGYAPNENL SNEELIRENY QGIRPAPGYP
ACPEHTEKAT IWELLEVEKH TGMKLTESFA MWPGASVSGW YFSHPDSKYY AVAQIQRDQV
EDYARRKGMS VTEVERWLAP NLGYDAD
Length

1,227

Mol. Wt

135.998 kDa

pI

4.8 (calculated)

Extinction coefficient

136,600 - 138,225 (calc based on 40 Y, 14 W, and 13 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

TypeResiduesDescriptionNotesReferences

Initiator Methionine

1

Removed

UniProt:P13009


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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:HOMOCYSMETB12-MONOMER

UniProt (EcoliWiki Page)

UniProt:P13009

PFAM (EcoliWiki Page)

PFAM:PF02574

RefSeq (EcoliWiki Page)

RefSeq:NP_418443


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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

metH

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Figure courtesy of RegulonDB

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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gbrowse_img.php?coord=4221831..4221871&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b4019 (EcoliWiki Page)

NCBI GEO profiles for metH

microarray

GenExpDB:b4019 (EcoliWiki Page)

Summary of data for metH from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to metH Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10587

EchoBASE (EcoliWiki Page)

EchoBASE:EB0582

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4019

EcoGene (EcoliWiki Page)

EcoGene:EG10587


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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000027053 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000016262 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00039583 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00010988 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000015753 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000017964 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-031001-5 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-557 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230138 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000023311 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000264178 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000013174 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000009254 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:894292 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000003622 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000023973 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000175300 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00010412001 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000039980 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

METH

From SHIGELLACYC

E. coli O157

METH

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02574


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Notes

Links

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References

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  7. ↑ 7.0 7.1 7.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 Taylor, R.T. and Weissbach, H. NS-methyltetrahydrofolate-homocysteine (Vitamin B12) methyltransferase (Escherichia coli B). Methods Enzymol. 17B (1971) 379-388.Taylor & Weissbach

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