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Gene |

Product(s) |

Expression|

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Standard Name	pflA
Gene Synonym(s)	ECK0893, b0902, JW0885, act^[1], act
Product Desc.	Pyruvate formate lyase I activase^[2]
Product Synonyms(s)	pyruvate formate lyase activating enzyme 1^[1], B0902^[3]^[1], Act^[3]^[1], PflA^[3]^[1] , act, ECK0893, JW0885, b0902
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pflA^[3]
Regulation/Activity
Quick Links
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Notes

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Radical SAM superfamily.^[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	pflA
Mnemonic	Pyruvate formate lyase
Synonyms	ECK0893, b0902, JW0885, act^[1], act
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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	20.47 minutes	MG1655: 950303..949563 <gbrowseImage> name=NC_000913:949563..950303 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 968173..967433 <gbrowseImage> name=NC_012967:967433..968173 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 852531..853271 <gbrowseImage> name=NC_012759:852531..853271 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 951502..950762 <gbrowseImage> name=NC_007779:950762..951502 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1004231..1003491 <gbrowseImage> name=NC_010473:1003491..1004231 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	949566	Edman degradation	PMID:3053170
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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
ΔpflA (Keio:JW0885)	deletion	deletion			PMID:16738554	Shigen CGSC8908^[4]
ΔpflA::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔpflA726::kan					PMID:16738554	CGSC:102300
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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
JW0885	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAGTTATTGGTCGCATTCA Primer 2:CCGAACATTACCTTATGACCGTA
13E3	Kohara Phage	Genobase	PMID:3038334
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[4]	est. P1 cotransduction: 90% ^[5] Synonyms:zbj-1230::Tn10
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[4]	est. P1 cotransduction: 8% ^[5]
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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:EG10028	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10028	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000025	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945517	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0027	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003068	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	PflA
Synonyms	pyruvate formate lyase activating enzyme 1^[1], B0902^[3]^[1], Act^[3]^[1], PflA^[3]^[1] , act, ECK0893, JW0885, b0902
Product description	Pyruvate formate lyase I activase^[2]
EC number (for enzymes)	1.97.1.4^[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:IPR007197	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	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:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0119	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006006	glucose metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0313	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006800	oxygen and reactive oxygen species metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001989	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001989	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043365	(formate-C-acetyltransferase)-activating enzyme activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012838	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043365	(formate-C-acetyltransferase)-activating enzyme activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.97.1.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007197	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001989	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001989	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012838	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
	GO:0016491	oxidoreductase activity	PMID:19711960	IDA: Inferred from Direct Assay		F	Fig. 2 illustrates that the over-expression of PflA allows for greater use of iron-sulfur clusters in anaerobic environments.	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	matC	PMID:16606699	Experiment(s):EBI-1138307
Protein	nadE	PMID:16606699	Experiment(s):EBI-1138307
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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 MSVIGRIHSF ESCGTVDGPG IRFITFFQGC LMRCLYCHNR DTWDTHGGKE VTVEDLMKEV VTYRHFMNAS GGGVTASGGE AILQAEFVRD WFRACKKEGI HTCLDTNGFV RRYDPVIDEL LEVTDLVMLD LKQMNDEIHQ NLVGVSNHRT LEFAKYLANK NVKVWIRYVV VPGWSDDDDS AHRLGEFTRD MGNVEKIELL PYHELGKHKW VAMGEEYKLD GVKPPKKETM ERVKGILEQY GHKVMF
Length	246
Mol. Wt	28.203 kDa
pI	6.4 (calculated)
Extinction coefficient	39,420 - 40,170 (calc based on 8 Y, 5 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
Initiator Methionine	1	Removed	UniProt:P0A9N4
Domain	24..184	PF04055 Radical SAM superfamily		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=pflA 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:16128869	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945517	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003068	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9N4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10028	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10028	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945517	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000025	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0027	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	2129	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	527	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	697	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)
pflA
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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_000913:950283..950323 source=MG1655 flip=1 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:b0902 (EcoliWiki Page)	NCBI GEO profiles for pflA
microarray	GenExpDB:b0902 (EcoliWiki Page)	Summary of data for pflA 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 (950214..950527) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:H11^[6]
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Notes

Accessions Related to pflA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10028	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0027	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0902
EcoGene	EcoGene:EG10028	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000025	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003068	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	PFLA	From SHIGELLACYC
E. coli O157	PFLA	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)	PF04055 Radical SAM superfamily
Superfamily (EcoliWiki Page)	SUPERFAMILY:102114
EcoCyc	EcoCyc:EG10028	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10028	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000025	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0027	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003068	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)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pflA:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

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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 pflA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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