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metC:On One Page

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Standard Name

metC

Gene Synonym(s)

ECK3000, b3008, JW2975, ecfA[1]

Product Desc.

MetC[2][3];

Component of CYSTATHIONINE-BETA-LYASE-CPLX[2]

Cystathionine beta-lyase; homotetrameric; cysteine desulfhydrase[4]

Product Synonyms(s)

cystathionine beta-lyase, PLP-dependent[1], B3008[2][1], EcfA[2][1], MetC[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): metC[2], OP00266

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(metC)    Textpresso(metC)

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Notes

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The Flint et al. N-terminal sequence is lacking the first four amino acids, probably due to in vitro proteolysis.[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

metC

Mnemonic

Methionine

Synonyms

ECK3000, b3008, JW2975, ecfA[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

67.9 minutes 

MG1655: 3150258..3151445
gbrowse_img.php?coord=3150258..3151445&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3086408..3087595
gbrowse_img.php?coord=3086408..3087595&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3150892..3152079
gbrowse_img.php?coord=3150892..3152079&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3248003..3249190
gbrowse_img.php?coord=3248003..3249190&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3037406..3038593
gbrowse_img.php?coord=3037406..3038593&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

ΔmetC (Keio:JW2975)

deletion

deletion

PMID:16738554

Shigen
CGSC10286[5]

metC162::Tn10

Insertion at 3,150,492 bp in MG1655 (NC_000913)

adapted from Nichols et al.[6]

CAG18475 = CGSC7435[5]

Synonyms:

metC69

CGSC:6457

metC162::Tn10

CGSC:7102

metC56

CGSC:9263

metC186

CGSC:9485

metC65

CGSC:23664

metC3158::Tn10kan

PMID:2540407

CGSC:38932

ΔmetC790::kan

PMID:16738554

CGSC:101828


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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

JW2975

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGGACAAAAAGCTTGATAC

Primer 2:CCTACAATTCGCGCAAAACCGGC

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[5]

est. P1 cotransduction: 13% [6]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[5]

est. P1 cotransduction: 34% [6]

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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:EG10583

EchoBASE (EcoliWiki Page)

EchoBASE:EB0578

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3008

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3742

EcoGene (EcoliWiki Page)

EcoGene:EG10583

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:METC

CGSC (EcoliWiki Page)

CGSC:514

ASAP (EcoliWikiPage)

ASAP:ABE-0009878


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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

MetC

Synonyms

cystathionine beta-lyase, PLP-dependent[1], B3008[2][1], EcfA[2][1], MetC[2][1]

Product description

MetC[2][3];

Component of CYSTATHIONINE-BETA-LYASE-CPLX[2]

Cystathionine beta-lyase; homotetrameric; cysteine desulfhydrase[4]

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: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:0004121

cystathionine beta-lyase activity

GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR006233
EC:4.4.1.8

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006233
SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0006520

amino acid metabolic process

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000277
InterPro:IPR006233

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:0016829

lyase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

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

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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 CYSTATHIONINE-BETA-LYASE-CPLX

could be indirect

Protein

ykgF

PMID:16606699

Experiment(s):EBI-1144540

Protein

groL

PMID:16606699

Experiment(s):EBI-1144540

Protein

slt

PMID:16606699

Experiment(s):EBI-1144540

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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 

MADKKLDTQL VNAGRSKKYT LGAVNSVIQR ASSLVFDSVE AKKHATRNRA NGELFYGRRG
TLTHFSLQQA MCELEGGAGC VLFPCGAAAV ANSILAFIEQ GDHVLMTNTA YEPSQDFCSK
ILSKLGVTTS WFDPLIGADI VKHLQPNTKI VFLESPGSIT MEVHDVPAIV AAVRSVVPDA
IIMIDNTWAA GVLFKALDFG IDVSIQAATK YLVGHSDAMI GTAVCNARCW EQLRENAYLM
GQMVDADTAY ITSRGLRTLG VRLRQHHESS LKVAEWLAEH PQVARVNHPA LPGSKGHEFW
KRDFTGSSGL FSFVLKKKLN NEELANYLDN FSLFSMAYSW GGYESLILAN QPEHIAAIRP
QGEIDFSGTL IRLHIGLEDV DDLIADLDAG FARIV
Length

395

Mol. Wt

43.212 kDa

pI

6.4 (calculated)

Extinction coefficient

46,410 - 47,160 (calc based on 9 Y, 6 W, and 6 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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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:CYSTATHIONINE-BETA-LYASE-MONOMER

UniProt (EcoliWiki Page)

UniProt:P06721

PFAM (EcoliWiki Page)

PFAM:PF01053

RefSeq (EcoliWiki Page)

RefSeq:NP_417481


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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)

metC

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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=3150238..3150278&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:b3008 (EcoliWiki Page)

NCBI GEO profiles for metC

microarray

GenExpDB:b3008 (EcoliWiki Page)

Summary of data for metC 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 (3149874..3150133) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:B9[9]

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Notes

Accessions Related to metC Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10583

EchoBASE (EcoliWiki Page)

EchoBASE:EB0578

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3008

EcoGene (EcoliWiki Page)

EcoGene:EG10583


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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

Monodelphis domestica

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

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YFR055W (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Shigella flexneri

METC

From SHIGELLACYC

E. coli O157

METC

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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 5.3 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 6.2 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 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. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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