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Expression|

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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] , ECK3000, JW2975, b3008
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): metC^[2], OP00266
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	67.9 minutes	MG1655: 3150258..3151445 <gbrowseImage> name=NC_000913:3150258..3151445 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3086408..3087595 <gbrowseImage> name=NC_012967:3086408..3087595 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3037406..3038593 <gbrowseImage> name=NC_012759:3037406..3038593 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3150892..3152079 <gbrowseImage> name=NC_007779:3150892..3152079 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3248003..3249190 <gbrowseImage> name=NC_010473:3248003..3249190 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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 Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	3150261	Edman degradation	PMID:3513164 PMID:8663055
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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.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
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 Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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

Resource	Resource Type	Source	Notes/Reference
JW2975	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCGGACAAAAAGCTTGATAC Primer 2:CCTACAATTCGCGCAAAACCGGC
5C10	Kohara Phage	Genobase	PMID:3038334
6H4	Kohara Phage	Genobase	PMID:3038334
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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10583	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000576	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946240	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0578	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009878	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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] , ECK3000, JW2975, b3008
Product description	MetC^[2]^[3]; Component of CYSTATHIONINE-BETA-LYASE-CPLX^[2] Cystathionine beta-lyase; homotetrameric; cysteine desulfhydrase^[4]
EC number (for enzymes)	4.4.1.8^[1]
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Notes

Function

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

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015422	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004121	cystathionine beta-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006233	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004121	cystathionine beta-lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.4.1.8	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006233	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000277	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006233	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009086	methionine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0486	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000277	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015422	F	Seeded from EcoCyc (v14.0)	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 Type	Partner	Notes	References	Evidence
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.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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

Name
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.

Type	Residues	Description	Notes	References
Domain	7..392	PF01053 Cys/Met metabolism PLP-dependent enzyme		PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=metC taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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 type	Source	Notes/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.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130906	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946240	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009878	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06721	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10583	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10583	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946240	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000576	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0578	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	596	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	1256	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	7277	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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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

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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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<protect><gbrowseImage> name=NC_000913:3150238..3150278 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
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 Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (3149874..3150133) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:B9^[7]
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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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10583	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0578	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3008
EcoGene	EcoGene:EG10583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000576	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009878	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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.

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01053 Cys/Met metabolism PLP-dependent enzyme
Panther (EcoliWiki Page)	PTHR11808:SF8
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:EG10583	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000576	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0578	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009878	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^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)
↑ ^2.00 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ ^5.0 ^5.1 ^5.2 ^5.3 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

metC:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to metC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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