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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	tdcE
Gene Synonym(s)	ECK3103, b3114, JW5522, yhaS^[1], yhaS
Product Desc.	Pyruvate formate-lyase/ketobutyrate formate-lyase^[2]
Product Synonyms(s)	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase^[1], B3114^[3]^[1], YhaS^[3]^[1], 2-ketobutyrate formate-lyase, active^[3]^[1], pyruvate formate-lyase 4^[3]^[1], PFL4^[3]^[1] , ECK3103, JW5522, yhaS, b3114
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): tdcABCDEFG^[3], OP00167, tdcABC
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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HT_Cmplx9_Cyt: YfiD+TdcE.^[2]

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	tdcE
Mnemonic	Threonine dehydratase, catabolic
Synonyms	ECK3103, b3114, JW5522, yhaS^[1], yhaS
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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	70.22 minutes	MG1655: 3260440..3258146 <gbrowseImage> name=NC_000913:3258146..3260440 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3195452..3193158 <gbrowseImage> name=NC_012967:3193158..3195452 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3145294..3147588 <gbrowseImage> name=NC_012759:3145294..3147588 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3261074..3258780 <gbrowseImage> name=NC_007779:3258780..3261074 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3358185..3355891 <gbrowseImage> name=NC_010473:3355891..3358185 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
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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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔtdcE (Keio:JW5522)	deletion	deletion			PMID:16738554	Shigen
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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
JW5522	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGGTAGATATTGATACCAG Primer 2:CCGAGCGCCTGGGTAAAGGTACG
21D1	Kohara Phage	Genobase	PMID:3038334
8F8	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: 16% ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: 1% ^[5] Synonyms:zgj-203::Tn10, zha-203::Tn10
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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:G7627	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004178	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947623	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2612	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010242	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	TdcE
Synonyms	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase^[1], B3114^[3]^[1], YhaS^[3]^[1], 2-ketobutyrate formate-lyase, active^[3]^[1], pyruvate formate-lyase 4^[3]^[1], PFL4^[3]^[1] , ECK3103, JW5522, yhaS, b3114
Product description	Pyruvate formate-lyase/ketobutyrate formate-lyase^[2]
EC number (for enzymes)	2.3.1.54^[1]
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Notes

Function

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<protect> Gene Ontology

KETOBUTFORMLY-MONOMER

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:IPR001150	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004184	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005949	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:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005949	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006006	glucose metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004184	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001150	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008415	acyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0012	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008861	formate C-acetyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004184	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008861	formate C-acetyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005949	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043875	2-ketobutyrate formate-lyase activity	PMID:9484901	IGI: Inferred from Genetic Interaction	EcoliWiki:pflB	F		complete
	GO:0005737	cytoplasm	PMID:9484901	IDA: Inferred from Direct Assay		C		complete
	GO:0070689	threonine catabolic process to propionate	PMID:9484901	IC: Inferred by Curator	GO:0043875	P		complete
	GO:0005624	membrane fraction	PMID:16858726	IDA: Inferred from Direct Assay		C		complete
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Interactions

KETOBUTFORMLY-MONOMER

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
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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
cytoplasm			From EcoCyc^[6]
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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 MKVDIDTSDK LYADAWLGFK GTDWKNEINV RDFIQHNYTP YEGDESFLAE ATPATTELWE KVMEGIRIEN ATHAPVDFDT NIATTITAHD AGYINQPLEK IVGLQTDAPL KRALHPFGGI NMIKSSFHAY GREMDSEFEY LFTDLRKTHN QGVFDVYSPD MLRCRKSGVL TGLPDGYGRG RIIGDYRRVA LYGISYLVRE RELQFADLQS RLEKGEDLEA TIRLREELAE HRHALLQIQE MAAKYGFDIS RPAQNAQEAV QWLYFAYLAA VKSQNGGAMS LGRTASFLDI YIERDFKAGV LNEQQAQELI DHFIMKIRMV RFLRTPEFDS LFSGDPIWAT EVIGGMGLDG RTLVTKNSFR YLHTLHTMGP APEPNLTILW SEELPIAFKK YAAQVSIVTS SLQYENDDLM RTDFNSDDYA IACCVSPMVI GKQMQFFGAR ANLAKTLLYA INGGVDEKLK IQVGPKTAPL MDDVLDYDKV MDSLDHFMDW LAVQYISALN IIHYMHDKYS YEASLMALHD RDVYRTMACG IAGLSVATDS LSAIKYARVK PIRDENGLAV DFEIDGEYPQ YGNNDERVDS IACDLVERFM KKIKALPTYR NAVPTQSILT ITSNVVYGQK TGNTPDGRRA GTPFAPGANP MHGRDRKGAV ASLTSVAKLP FTYAKDGISY TFSIVPAALG KEDPVRKTNL VGLLDGYFHH EADVEGGQHL NVNVMNREML LDAIEHPEKY PNLTIRVSGY AVRFNALTRE QQQDVISRTF TQAL
Length	764
Mol. Wt	85.937 kDa
pI	5.6 (calculated)
Extinction coefficient	92,140 - 92,765 (calc based on 36 Y, 7 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.

Type	Residues	Description	References
Domain	634..745	PF01228 Glycine radical	PMID:19920124
Domain	22..618	PF02901 Pyruvate formate lyase	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=tdcE 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:49176316	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947623	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010242	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P42632	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7627	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12758	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947623	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004178	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2612	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	88	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	15	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	49	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)
tdcABCDEFG
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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_000913:3260420..3260460 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3114 (EcoliWiki Page)	NCBI GEO profiles for tdcE
microarray	GenExpDB:b3114 (EcoliWiki Page)	Summary of data for tdcE 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
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Notes

Accessions Related to tdcE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7627	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2612	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3114
EcoGene	EcoGene:EG12758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004178	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010242	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
Shigella flexneri	TDCE	From SHIGELLACYC
E. coli O157	TDCE	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)	PF01228 Glycine radical
Superfamily (EcoliWiki Page)	SUPERFAMILY:51998
Pfam (EcoliWiki Page)	PF02901 Pyruvate formate lyase
EcoCyc	EcoCyc:G7627	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004178	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2612	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010242	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 ^1.11 ^1.12 ^1.13 ^1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

tdcE: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

KETOBUTFORMLY-MONOMER

KETOBUTFORMLY-MONOMER

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 tdcE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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