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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	fdhF
Gene Synonym(s)	ECK4072, b4079, JW4040, chlF^[1]
Product Desc.	FORMATEDEHYDROGH^[2]^[3]; Component of formate hydrogenlyase complex^[2]^[3] Formate dehydrogenase H, selenopeptide; molybdate dependence; part of FHL-1 and FHL-2 (formate hydrogenlyase) complexes^[4]
Product Synonyms(s)	formate dehydrogenase-H, selenopolypeptide subunit^[1], B4079^[2]^[1], ChlF^[2]^[1], FdhF^[2]^[1], FDH-H^[2]^[1] , ECK4072, JW4040, b4079
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): fdhF^[2], OP00207
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 UGA stop codon 140 is translated as selenocysteine in vivo and indicated as a "U" in the protein sequence.^[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	fdhF
Mnemonic	Formate dehydrogenase
Synonyms	ECK4072, b4079, JW4040, chlF^[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	92.58 minutes	MG1655: 4297389..4295242 <gbrowseImage> name=NC_000913:4295242..4297389 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4278188..4276041 <gbrowseImage> name=NC_012967:4276041..4278188 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4233977..4236124 <gbrowseImage> name=NC_012759:4233977..4236124 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4302845..4300698 <gbrowseImage> name=NC_007779:4300698..4302845 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4397751..4395604 <gbrowseImage> name=NC_010473:4395604..4397751 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	4295242	Edman degradation	PMID:2211698
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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
ΔfdhF (Keio:JW4040)	deletion	deletion			PMID:16738554	Shigen CGSC10908^[5]
ΔfdhF774::kan					PMID:16738554	CGSC:100800
chlF in strain PK 27			Enzyme Activity	Lack of formate nitrate reductase enzyme activity	PMID:4558444	Strain: PK 27	Table 7
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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
JW4040	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAAGTCGTCACGGTTTG Primer 2:CCgGCCAGTGCCGCTTCGCGCAG
10G7	Kohara Phage	Genobase	PMID:3038334
1A11	Kohara Phage	Genobase	PMID:3038334
12A6	Kohara Phage	Genobase	PMID:3038334
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 7% ^[6]
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 70% ^[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:EG10285	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10285	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000279	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948584	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0281	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013363	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	FdhF
Synonyms	formate dehydrogenase-H, selenopolypeptide subunit^[1], B4079^[2]^[1], ChlF^[2]^[1], FdhF^[2]^[1], FDH-H^[2]^[1] , ECK4072, JW4040, b4079
Product description	FORMATEDEHYDROGH^[2]^[3]; Component of formate hydrogenlyase complex^[2]^[3] Formate dehydrogenase H, selenopeptide; molybdate dependence; part of FHL-1 and FHL-2 (formate hydrogenlyase) complexes^[4]
EC number (for enzymes)	1.2.1.2^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009010	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:0008430	selenium binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0711	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008863	formate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006478	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008863	formate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.2.1.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006655	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009326	formate dehydrogenase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006478	C	Seeded from EcoCyc (v14.0)	complete
	GO:0015942	formate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006478	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006655	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006656	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006657	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006963	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:0030151	molybdenum ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006657	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030151	molybdenum ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0500	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: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: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:IPR006478	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
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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 formate hydrogenlyase complex	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1147409
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1147409
Protein	ygiT		PMID:16606699	Experiment(s):EBI-1147409
Protein	rpsE		PMID:16606699	Experiment(s):EBI-1147409
Protein	rplM		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsT		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsH		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplU		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsS		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsR		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsM		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsD		PMID:19402753	LCMS(ID Probability):99.6
Protein	yfiF		PMID:19402753	LCMS(ID Probability):99.6
Protein	deaD		PMID:19402753	LCMS(ID Probability):99.6
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</protect>

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
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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 MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD FINDTQILTP RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP DAIQTTGSSR GTGNETNYVM QKFARAVIGT NNVDCCARVU HGPSVAGLHQ SVGNGAMSNA INEIDNTDLV FVFGYNPADS HPIVANHVIN AKRNGAKIIV CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY DKAFVASRTE GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT YPGYQYVKDP ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI MGEDPLQTDA ELSAVRKAFE DLELVIVQDI FMTKTASAAD VILPSTSWGE HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ IISEIATRMG YPMHYNNTQE IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT SYLFKEKFDT PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI YMTYQWWIGA CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID EYNKLKTRLR EAALA
Length	714
Mol. Wt	79.223 kDa
pI	6.3 (calculated)
Extinction coefficient	117,690 - 119,565 (calc based on 31 Y, 13 W, and 15 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	1..54	PF04879 Molybdopterin oxidoreductase Fe4S4 domain	PMID:19920124
Domain	61..488	PF00384 Molybdopterin oxidoreductase	PMID:19920124
Domain	575..682	PF01568 Molydopterin dinucleotide binding 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=fdhF 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:16131905	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948584	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013363	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P07658	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10285	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10285	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948584	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000279	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0281	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	Notes	Reference(s)
Protein	E. coli K-12 MG1655	3^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	1	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
fdhF
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Figure courtesy of RegulonDB

</protect>

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_000913:4297369..4297409 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:b4079 (EcoliWiki Page)	NCBI GEO profiles for fdhF
microarray	GenExpDB:b4079 (EcoliWiki Page)	Summary of data for fdhF 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 (4296875..4297161) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:A5^[7]
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Notes

Accessions Related to fdhF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10285	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0281	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4079
EcoGene	EcoGene:EG10285	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000279	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013363	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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</protect>

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)	PF04879 Molybdopterin oxidoreductase Fe4S4 domain
Pfam (EcoliWiki Page)	PF01568 Molydopterin dinucleotide binding domain
Pfam (EcoliWiki Page)	PF00384 Molybdopterin oxidoreductase
Superfamily (EcoliWiki Page)	SUPERFAMILY:50692
Superfamily (EcoliWiki Page)	SUPERFAMILY:53706
EcoCyc	EcoCyc:EG10285	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10285	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000279	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0281	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013363	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 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 ^3.2 ^3.3 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

fdhF: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 fdhF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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