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Standard Name

metB

Gene Synonym(s)

ECK3931, b3939, JW3910, met-1[1]

Product Desc.

MetB[2][3];

Component of O-SUCCHOMOSERLYASE-CPLX[2]

Cystathionine gamma-synthase; homotetrameric[4]

Product Synonyms(s)

cystathionine gamma-synthase, PLP-dependent[1], B3939[2][1], MetB[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): metBL[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(metB)    Textpresso(metB)

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Notes

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Upregulated by GSNO in defined medium.[4]



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

metB

Mnemonic

Methionine

Synonyms

ECK3931, b3939, JW3910, met-1[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

88.94 minutes, 88.94 minutes 

MG1655: 4126695..4127855
gbrowse_img.php?coord=4126695..4127855&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4108779..4109939
gbrowse_img.php?coord=4108779..4109939&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3508009..3506849
gbrowse_img.php?coord=3506849..3508009&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4226392..4227552
gbrowse_img.php?coord=4226392..4227552&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 4016364..4017524
gbrowse_img.php?coord=4016364..4017524&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

ΔmetB (Keio:JW3910)

deletion

deletion

PMID:16738554

Shigen
CGSC10824[5]

metB1

PMID:14047235 PMID:16588691

CGSC:4538

metB65

CGSC:6823

metB0

CGSC:9934

metB185

CGSC:10292

ΔmetB726::kan

PMID:16738554

CGSC:101826

overexpression in a metC mutant

Growth Phenotype

Suppresses diaminopimelate requirement of dapA, dapB, and dapD

PMID:8262915

meso-lanthionine and L-allo-cystathionine are produced and incorporated into peptidoglycan

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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3910

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGCGTAAACAGGCCACCAT

Primer 2:CCgCCCTTGTTTGCAGCCCGGAA

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[5]

est. P1 cotransduction: 4% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 56% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG10582

EchoBASE (EcoliWiki Page)

EchoBASE:EB0577

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3939

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4892

EcoGene (EcoliWiki Page)

EcoGene:EG10582

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:METB

CGSC (EcoliWiki Page)

CGSC:515

ASAP (EcoliWikiPage)

ASAP:ABE-0012887


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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

MetB

Synonyms

cystathionine gamma-synthase, PLP-dependent[1], B3939[2][1], MetB[2][1]

Product description

MetB[2][3];

Component of O-SUCCHOMOSERLYASE-CPLX[2]

Cystathionine gamma-synthase; homotetrameric[4]

EC number (for enzymes) 
2.5.1.48[1]
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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:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P18843

F

Seeded from EcoCyc [7]

complete

GO:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421
InterPro:IPR015422

F

Seeded from EcoCyc [7]

complete

GO:0003962

cystathionine gamma-synthase activity

GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.5.1.48

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0006520

amino acid metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000277

P

Seeded from EcoCyc [7]

complete

GO:0008652

amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0028

P

Seeded from EcoCyc [7]

complete

GO:0009086

methionine biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0486

P

Seeded from EcoCyc [7]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [7]

complete

GO:0030170

pyridoxal phosphate binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000277
InterPro:IPR015421
InterPro:IPR015422

F

Seeded from EcoCyc [7]

complete

GO:0009063

amino acid catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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

Subunits of O-SUCCHOMOSERLYASE-CPLX

could be indirect

Protein

nadE

PMID:16606699

Experiment(s):EBI-1147115

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Notes

metB1 is a mutant brought about by X-ray mutagenesis and is most likely a deletion mutation.

The metB1 mutation causes a requirement for methionine and produces no enzymatic activity. [9]

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 

MTRKQATIAV RSGLNDDEQY GCVVPPIHLS STYNFTGFNE PRAHDYSRRG NPTRDVVQRA
LAELEGGAGA VLTNTGMSAI HLVTTVFLKP GDLLVAPHDC YGGSYRLFDS LAKRGCYRVL
FVDQGDEQAL RAALAEKPKL VLVESPSNPL LRVVDIAKIC HLAREVGAVS VVDNTFLSPA
LQNPLALGAD LVLHSCTKYL NGHSDVVAGV VIAKDPDVVT ELAWWANNIG VTGGAFDSYL
LLRGLRTLVP RMELAQRNAQ AIVKYLQTQP LVKKLYHPSL PENQGHEIAA RQQKGFGAML
SFELDGDEQT LRRFLGGLSL FTLAESLGGV ESLISHAATM THAGMAPEAR AAAGISETLL
RISTGIEDGE DLIADLENGF RAANKG
Length

386

Mol. Wt

41.55 kDa

pI

6.4 (calculated)

Extinction coefficient

25,900 - 26,525 (calc based on 10 Y, 2 W, and 5 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
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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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource typeSourceNotes/Reference
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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:O-SUCCHOMOSERLYASE-MONOMER

UniProt (EcoliWiki Page)

UniProt:P00935

PFAM (EcoliWiki Page)

PFAM:PF01053

RefSeq (EcoliWiki Page)

RefSeq:NP_418374


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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)

metBL

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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=4126675..4126715&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:b3939 (EcoliWiki Page)

NCBI GEO profiles for metB

microarray

GenExpDB:b3939 (EcoliWiki Page)

Summary of data for metB 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

GFP Fusion

Intergenic region (4125675..4126058) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:C5[10]

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Notes

Accessions Related to metB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10582

EchoBASE (EcoliWiki Page)

EchoBASE:EB0577

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3939

EcoGene (EcoliWiki Page)

EcoGene:EG10582


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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

  • ENSANGP00000022045 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000006675 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT3G57050 (score: 1.000; bootstrap: 86%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000005788 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000019679 (score: 0.599)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00042787 (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00022856 (score: 1.000; bootstrap: 99%)
  • WBGene00009048 (score: 0.821)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000030288 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030131-774 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-3146 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-3587 (score: 0.998)
  • ZDB-CDNA-040905-4 (score: 0.771)
  • ZDB-GENE-040905-3 (score: 0.771)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0191318 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0000566 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18818-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000018469 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000235407 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000025387 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000000610 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1339968 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q94I44 (score: 1.000; bootstrap: 83%)
  • Q7XEY3 (score: 1.000; bootstrap: 85%)
  • Q94I39 (score: 0.905)
  • Q7XEX8 (score: 0.905)
  • Q94I45 (score: 0.777)
  • Q7XEY4 (score: 0.777)
  • Q67VG6 (score: 0.466)
  • Q8S7G4 (score: 0.353)
  • O04981 (score: 0.353)
  • O04982 (score: 0.346)
  • Q9FR94 (score: 0.299)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000001478 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000015049 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YAL012W (score: 1.000; bootstrap: 88%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC11E101 (score: 1.000; bootstrap: 79%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000173857 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00019855001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000024438 (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Shigella flexneri

METB

From SHIGELLACYC

E. coli O157

METB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01053


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Hall BG (1989) Selection, adaptation, and bacterial operons. Genome 31: 265-71 PubMed EcoliWiki page
  10. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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