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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	pdhR
Gene Synonym(s)	ECK0112, b0113, JW0109, yacB, aceC, genA, dcuA'^[1]^[2]
Product Desc.	PdhR transcriptional dual regulator^[2]^[3] Pyruvate dehydrogenase operon (pdhR-aceEF-lpd) repressor; autoregulatory; pyruvate relieves repression; monomeric^[4]
Product Synonyms(s)	DNA-binding transcriptional dual regulator^[1], B0113^[2]^[1], YacB^[2]^[1], GenA^[2]^[1], PdhR^[2]^[1] , aceC, ECK0112, genA, JW0109, yacB, b0113
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pdhR-aceEF-lpdA^[2]
Regulation/Activity
Quick Links
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Notes

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The N-terminus of overexpressed PdhR has been determined (Quail and Guest, 1995), indicating that the initial Met is removed. however, the native pdhR RBS was not used, so PdhR is not in the Verified Set, although this is probably the correct start. PdhR is a GntR-type DNA-binding transcriptional regulator.^[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	pdhR
Mnemonic	Pyruvate dehydrogenase
Synonyms	ECK0112, b0113, JW0109, yacB, aceC, genA, dcuA'^[1]^[2]
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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	2.63 minutes	MG1655: 122092..122856 <gbrowseImage> name=NC_000913:122092..122856 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 124896..125660 <gbrowseImage> name=NC_012967:124896..125660 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 122091..122855 <gbrowseImage> name=NC_012759:122091..122855 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 122092..122856 <gbrowseImage> name=NC_007779:122092..122856 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 96196..96960 <gbrowseImage> name=NC_010473:96196..96960 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
pdhR(del) (Keio:JW0109)	deletion	deletion			PMID:16738554	Shigen CGSC8391^[5]
pdhRR118C		R118C		(in ACEC816; constitutively activated)			Strain variation; seeded from UniProt:P0ACL9
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire Dextrin	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire D-Galactose	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire b-Methyl-D-glucoside	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire D-Sorbitol	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-1-phosphate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-6-phosphate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire DL-a-Glycerol	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire DL-Lactate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire L-Alanine	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire L-Alanyl-glycine	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire L-Serine	PMID:16095938
pdhR(del)::kan	deletion		Biolog:respiration	unable to respire Uridine	PMID:16095938
pdhR731(del)::kan					PMID:16738554	CGSC:102264
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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
JW0109	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCTACAGCAAAATCCGCCA Primer 2:CCATTCTTTCGTTGCTCCAGACG
4D12	Kohara Phage	Genobase	PMID:3038334
4E11	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 37% ^[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:EG11088	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11088	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001076	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944827	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1080	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000394	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	PdhR
Synonyms	DNA-binding transcriptional dual regulator^[1], B0113^[2]^[1], YacB^[2]^[1], GenA^[2]^[1], PdhR^[2]^[1] , aceC, ECK0112, genA, JW0109, yacB, b0113
Product description	PdhR transcriptional dual regulator^[2]^[3] Pyruvate dehydrogenase operon (pdhR-aceEF-lpd) repressor; autoregulatory; pyruvate relieves repression; monomeric^[4]
EC number (for enzymes)
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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:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000524	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:2060763	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P10585 UniProtKB:P0A8V6 UniProtKB:P12380 UniProtKB:P22773	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:7783622	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:8057842	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:8262214	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000524	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:2060763	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P10585 UniProtKB:P0A8V6 UniProtKB:P12380 UniProtKB:P22773	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:7783622	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:8057842	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:8262214	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:2060763	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P10585 UniProtKB:P0A8V6 UniProtKB:P12380 UniProtKB:P22773	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:7783622	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:8057842	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:8262214	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:2060763	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P10585 UniProtKB:P0A8V6 UniProtKB:P12380 UniProtKB:P22773	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:7783622	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:8057842	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:8262214	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:2060763	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P10585 UniProtKB:P0A8V6 UniProtKB:P12380 UniProtKB:P22773	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:7783622	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:8057842	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:8262214	IDA: Inferred from Direct Assay		P	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	References	Evidence
Protein	aceF	PMID:16606699	Experiment(s):EBI-1135589
Protein	tatE	PMID:16606699	Experiment(s):EBI-1135589
Protein	rpmB	PMID:16606699	Experiment(s):EBI-1135589
Protein	aceE	PMID:16606699	Experiment(s):EBI-1135589
Protein	lpdA	PMID:16606699	Experiment(s):EBI-1135589
Protein	groL	PMID:16606699	Experiment(s):EBI-1135589
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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 MAYSKIRQPK LSDVIEQQLE FLILEGTLRP GEKLPPEREL AKQFDVSRPS LREAIQRLEA KGLLLRRQGG GTFVQSSLWQ SFSDPLVELL SDHPESQYDL LETRHALEGI AAYYAALRST DEDKERIREL HHAIELAQQS GDLDAESNAV LQYQIAVTEA AHNVVLLHLL RCMEPMLAQN VRQNFELLYS RREMLPLVSS HRTRIFEAIM AGKPEEAREA SHRHLAFIEE ILLDRSREES RRERSLRRLE QRKN
Length	254
Mol. Wt	29.426 kDa
pI	6.4 (calculated)
Extinction coefficient	14,440 - 14,565 (calc based on 6 Y, 1 W, and 1 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	11..74	PF00392 Bacterial regulatory proteins, gntR family	PMID:19920124
Domain	99..227	PF07729 FCD domain	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=pdhR taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16128106	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944827	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000394	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACL9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11088	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11088	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944827	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001076	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1080	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	2126	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	270	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	1008	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)
pdhR-aceEF-lpdA
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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_000913:122072..122112 source=MG1655 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:b0113 (EcoliWiki Page)	NCBI GEO profiles for pdhR
microarray	GenExpDB:b0113 (EcoliWiki Page)	Summary of data for pdhR 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 (121453..122099) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:A7^[7]
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Notes

Accessions Related to pdhR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11088	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1080	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0113
EcoGene	EcoGene:EG11088	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001076	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000394	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	PDHR	From SHIGELLACYC
E. coli O157	PDHR	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF07729 FCD domain
Pfam (EcoliWiki Page)	PF00392 Bacterial regulatory proteins, gntR family
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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 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 ^2.11 ^2.12 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 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pdhR: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 pdhR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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