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Product(s) |

Expression|

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Standard Name	fdnH
Gene Synonym(s)	ECK1469, b1475, JW1471^[1], JW1471
Product Desc.	formate dehydrogenase N, β subunit^[2]^[3]; Component of trimer complex of formate dehydrogenase-N α, β and γ subunits^[2]^[3]; formate dehydrogenase-N^[2]^[3] Formate dehydrogenase-N, Fe-S subunit, anaerobic; periplasmic^[4]
Product Synonyms(s)	formate dehydrogenase-N, Fe-S (beta) subunit, nitrate-inducible^[1], B1475^[2]^[1], FdnH^[2]^[1] , ECK1469, JW1471, b1475
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): fdnGHI^[2], OP00216
Regulation/Activity
Quick Links
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Notes

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FdnH is co-exported bound to Tat substrate FdnG. HT_Cmplx12_Mem: FdnG+FdnH.^[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	fdnH
Mnemonic	Formate dehydrogenase-N
Synonyms	ECK1469, b1475, JW1471^[1], JW1471
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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	33.37 minutes	MG1655: 1548485..1549369 <gbrowseImage> name=NC_000913:1548485..1549369 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1524611..1525495 <gbrowseImage> name=NC_012967:1524611..1525495 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1440544..1441428 <gbrowseImage> name=NC_012759:1440544..1441428 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1552175..1553059 <gbrowseImage> name=NC_007779:1552175..1553059 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1639080..1639964 <gbrowseImage> name=NC_010473:1639080..1639964 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)	Reference	Availability	Comments
ΔfdnH (Keio:JW1471)	deletion	deletion	PMID:16738554	Shigen
fdnH::Tn5KAN-2 (FB20331)	Insertion at nt 360 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20331	does not contain pKD46
fdnH::Tn5KAN-2 (FB20332)	Insertion at nt 360 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20332	contains pKD46
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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
JW1471	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTATGGAAACGCAGGACAT Primer 2:CCtTCATGATGATCCTCCTCGTC
1G9	Kohara Phage	Genobase	PMID:3038334
9B8	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: 64% ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdh-925::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:EG11228	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11228	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001206	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948794	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1210	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004919	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	FdnH
Synonyms	formate dehydrogenase-N, Fe-S (beta) subunit, nitrate-inducible^[1], B1475^[2]^[1], FdnH^[2]^[1] , ECK1469, JW1471, b1475
Product description	formate dehydrogenase N, β subunit^[2]^[3]; Component of trimer complex of formate dehydrogenase-N α, β and γ subunits^[2]^[3]; formate dehydrogenase-N^[2]^[3] Formate dehydrogenase-N, Fe-S subunit, anaerobic; periplasmic^[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: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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008863	formate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006470	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009061	anaerobic respiration	PMID:1099093	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0009326	formate dehydrogenase complex	PMID:11752799	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006470	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9904	C	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045333	cellular respiration	PMID:5996	IDA: Inferred from Direct Assay		P	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:IPR017900	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
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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 trimer complex of formate dehydrogenase-N α, β and γ subunits	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1139940
Protein	rplB		PMID:16606699	Experiment(s):EBI-1139940
Protein	corC		PMID:16606699	Experiment(s):EBI-1139940
Protein	tufB		PMID:19402753	MALDI(Z-score):19.015549
Protein	fdhE		PMID:19402753	MALDI(Z-score):39.840430
Protein	fdoG		PMID:19402753	MALDI(Z-score):17.792570
Protein	Subunits of formate dehydrogenase-N	could be indirect
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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
plasma membrane			From EcoCyc^[3]
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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 MAMETQDIIK RSATNSITPP SQVRDYKAEV AKLIDVSTCI GCKACQVACS EWNDIRDEVG HCVGVYDNPA DLSAKSWTVM RFSETEQNGK LEWLIRKDGC MHCEDPGCLK ACPSAGAIIQ YANGIVDFQS ENCIGCGYCI AGCPFNIPRL NKEDNRVYKC TLCVDRVSVG QEPACVKTCP TGAIHFGTKK EMLELAEQRV AKLKARGYEH AGVYNPEGVG GTHVMYVLHH ADQPELYHGL PKDPKIDTSV SLWKGALKPL AAAGFIATFA GLIFHYIGIG PNKEVDDDEE DHHE
Length	294
Mol. Wt	32.237 kDa
pI	5.9 (calculated)
Extinction coefficient	36,900 - 39,025 (calc based on 10 Y, 4 W, and 17 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	246..290	PF09163 Formate dehydrogenase N, transmembrane		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=fdnH 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:16129434	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948794	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004919	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAJ3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11228	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11228	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948794	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001206	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1210	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	2^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^a	molecules/cell/generation	Medium: MOPS Minimal 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	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)
fdnGHI
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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_000913:1548465..1548505 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:b1475 (EcoliWiki Page)	NCBI GEO profiles for fdnH
microarray	GenExpDB:b1475 (EcoliWiki Page)	Summary of data for fdnH 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 fdnH Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11228	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1210	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1475
EcoGene	EcoGene:EG11228	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001206	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004919	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
Xenopus tropicalis	ENSXETP00000000543 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	FDNH	From SHIGELLACYC
E. coli O157	FDNH	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
Panther (EcoliWiki Page)	PTHR11938:SF10
Superfamily (EcoliWiki Page)	SUPERFAMILY:54862
Pfam (EcoliWiki Page)	PF09163 Formate dehydrogenase N, transmembrane
EcoCyc	EcoCyc:EG11228	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11228	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001206	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1210	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004919	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 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 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).

fdnH:On One Page

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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 fdnH Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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