fnr:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

fnr

Gene Synonym(s)

ECK1330, b1334, JW1328, nirA, nirR, ossA, oxrA[1][2]

Product Desc.

FNR transcriptional dual regulator[2][3]

Global transcription factor for anaerobic growth; [4FE-4S] cluster; homodimeric[4]

Product Synonyms(s)

DNA-binding transcriptional dual regulator, global regulator of anaerobic growth[1], B1334[2][1], Fnr[2][1], OssA[2][1], NirR[2][1], NirA[2][1], transcriptional regulation of aerobic, anaerobic respiration, osmotic balance[2][1], OxrA[2][1] , ECK1330, JW1328, nirA, nirR, ossA, b1334

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): fnr[2], OP00029

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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FNR represses genes involved in aerobic respiration and activates genes required for anaerobic respiration.[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

fnr

Mnemonic

fumurate and nitrate reductase Fumarate and nitrate reduction

Synonyms

ECK1330, b1334, JW1328, nirA, nirR, ossA, oxrA[1][2]

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Notes

The fnr gene was identified in 1976 by Lambden and Guest [5] who isolated mutants of E. coli K-12 that were unable to use fumarate as an anaerobic electron acceptor.

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

30.11 minutes 

MG1655: 1397550..1396798
<gbrowseImage> name=NC_000913:1396798..1397550 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1396696..1395944
<gbrowseImage> name=NC_012967:1395944..1396696 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1287647..1288399
<gbrowseImage> name=NC_012759:1287647..1288399 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1401240..1400488
<gbrowseImage> name=NC_007779:1400488..1401240 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1486946..1486194
<gbrowseImage> name=NC_010473:1486194..1486946 source=DH10B preset=GeneLocation </gbrowseImage>

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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

1396798

Edman degradation

PMID:2181237


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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

fnr(del) (Keio:JW1328)

deletion

deletion

PMID:16738554

Shigen

CGSC9187[6]

fnrD154A,G,V

D154A,G,V

Loss of regulation by O(2)

seeded from UniProt:P0A9E5

fnr::Tn5KAN-I-SceI (FB20296)

Insertion at nt 606 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20296

does not contain pKD46

fnrC16A

C16A

No effect

PMID:2226775

published as fnr-382

seeded from UniProt:P0A9E5

fnrC20S

C20S

Loss of activity

PMID:2226775

published as fnr-197

seeded from UniProt:P0A9E5

fnrD22G

D22G

Loss of regulation by O(2)

seeded from UniProt:P0A9E5

fnrS73F

S73F

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrE64Q

E64Q

No effect

seeded from UniProt:P0A9E5

fnrR72H

R72H

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrI81T

I81T

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrG85A

G85A

Decrease in activity; no effect on DNA-binding. Trace activity; when associated with P-187

seeded from UniProt:P0A9E5

fnrD86A

D86A

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrE87K

E87K

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrQ88E

Q88E

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrH93R

H93R

Loss of regulation by O(2)

seeded from UniProt:P0A9E5

fnrG96D

G96D

Loss of activity

seeded from UniProt:P0A9E5

fnrT118A,P

T118A,P

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrM120I,R,T,V

M120I,R,T,V

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrC122A,S

C122A,S

Loss of activity

seeded from UniProt:P0A9E5

fnrR140A

R140A

Decrease in activity

seeded from UniProt:P0A9E5

fnrM143A

M143A

Decrease in activity

seeded from UniProt:P0A9E5

fnrM144A

M144A

Decrease in activity due to faulty dimerization

seeded from UniProt:P0A9E5

fnrR145A

R145A

Decrease in activity

seeded from UniProt:P0A9E5

fnrL146A

L146A

Decrease in activity

seeded from UniProt:P0A9E5

fnrM147A

M147A

Decrease in activity due to faulty dimerization

seeded from UniProt:P0A9E5

fnrE150K

E150K

Loss of regulation by O(2)

seeded from UniProt:P0A9E5

fnrT82P

T82P

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrI151A

I151A

Decrease in activity due to faulty dimerization

seeded from UniProt:P0A9E5

fnrC29G

C29G

Loss of activity

seeded from UniProt:P0A9E5

fnrD43G

D43G

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrI158A

I158A

Decrease in activity due to faulty dimerization

seeded from UniProt:P0A9E5

fnrF181L

F181L

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrF186S

F186S

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrS187P

S187P

Decrease in activity; no effect on DNA-binding. Trace activity; when associated with A-85

seeded from UniProt:P0A9E5

fnrF191L

F191L

Decrease in activity; no effect on DNA-binding

seeded from UniProt:P0A9E5

fnrC23G

C23G

Loss of activity

PMID:2226775

published as fnr-383

seeded from UniProt:P0A9E5

fnrL28H

L28H

Loss of regulation by O(2)

seeded from UniProt:P0A9E5

fnr(del)::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938

D154A

D154A

Constitutive dimerization

PMID:16959764

fnr-1

CGSC:6526

fnr-25

CGSC:7473

fnr-267(del)

CGSC:80710

fnr-771(del)::kan

PMID:16738554

CGSC:100976

fnr -

Sensitivity to

Mutants were sensitive to minimun 5 mM of chlorate.

PMID:7047497


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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

JW1328

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCCCGGAAAAGCGAATTAT

Primer 2:CCGGCAACGTTACGCGTATGACC

6B4

Kohara Phage

Genobase

PMID:3038334

3G3

Kohara Phage

Genobase

PMID:3038334

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[6]

est. P1 cotransduction: 34% [7]
Synonyms:zci-233::Tn10

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[6]

est. P1 cotransduction: 62% [7]
Synonyms:zcj-3061::Tn10, zda-3061::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:EG10325

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10325

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000319

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945908

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0321

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004475

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Fnr

Synonyms

DNA-binding transcriptional dual regulator, global regulator of anaerobic growth[1], B1334[2][1], Fnr[2][1], OssA[2][1], NirR[2][1], NirA[2][1], transcriptional regulation of aerobic, anaerobic respiration, osmotic balance[2][1], OxrA[2][1] , ECK1330, JW1328, nirA, nirR, ossA, b1334

Product description

FNR transcriptional dual regulator[2][3]

Global transcription factor for anaerobic growth; [4FE-4S] cluster; homodimeric[4]

EC number (for enzymes)


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Notes

FNR is a global regulator, belonging to the CRP superfamily of helix turn helix DNA binding proteins. FNR is active under anaerobic conditions and depending on the location of the binding site, either activates or represses genes. The oxygen sensing function of FNR is mediated by a [4Fe-4S] cluster. The [4Fe-4S] cluster is ligated to Cys20, 23, 29 and 122, is stable anaerobically and promotes FNR dimerization. In the presence of oxygen, the cluster is converted to a [2Fe-2S] cluster decreasing FNR dimerization, DNA binding and inactivating FNR.

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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012318

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001808

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018335

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:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001808

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018335

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:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001808

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018335

P

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012318

P

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0805

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: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

phoB

PMID:16606699

Experiment(s):EBI-1139571

Protein

nadE

PMID:16606699

Experiment(s):EBI-1139571

Protein

prs

PMID:16606699

Experiment(s):EBI-1139571

Protein

matC

PMID:16606699

Experiment(s):EBI-1139571

Protein

self

detectable dimerization requires ligation of the [4Fe-4S] cluster


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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[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 

MIPEKRIIRR IQSGGCAIHC QDCSISQLCI PFTLNEHELD QLDNIIERKK PIQKGQTLFK
AGDELKSLYA IRSGTIKSYT ITEQGDEQIT GFHLAGDLVG FDAIGSGHHP SFAQALETSM
VCEIPFETLD DLSGKMPNLR QQMMRLMSGE IKGDQDMILL LSKKNAEERL AAFIYNLSRR
FAQRGFSPRE FRLTMTRGDI GNYLGLTVET ISRLLGRFQK SGMLAVKGKY ITIENNDALA
QLAGHTRNVA
Length

250

Mol. Wt

27.968 kDa

pI

8.1 (calculated)

Extinction coefficient

7,450 - 8,075 (calc based on 5 Y, 0 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 Notes References

Domain

49..138

PF00027 Cyclic nucleotide-binding domain

PMID:19920124

Domain

193..224

PF00325 Bacterial regulatory proteins, crp family

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=fnr 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:16129295

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945908

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004475

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9E5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10325

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10325

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945908

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000319

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0321

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 MC4100

4.53E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

6551

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

2582

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

2504

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

fnr

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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_000913:1397530..1397570 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:b1334 (EcoliWiki Page)

NCBI GEO profiles for fnr

microarray

GenExpDB:b1334 (EcoliWiki Page)

Summary of data for fnr 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 fnr Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10325

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0321

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1334

EcoGene

EcoGene:EG10325

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000319

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004475

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Homo sapiens

  • ENSP00000346628 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000014642 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

FNR

From SHIGELLACYC

E. coli O157

FNR

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF00325 Bacterial regulatory proteins, crp family

Pfam (EcoliWiki Page)

PF00027 Cyclic nucleotide-binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:46785

Superfamily (EcoliWiki Page)

SUPERFAMILY:51206

EcoCyc

EcoCyc:EG10325

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10325

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000319

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0321

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004475

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 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 1.15 1.16 1.17 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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 2.13 2.14 2.15 2.16 2.17 2.18 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ Lambden, PR & Guest, JR (1976) Mutants of Escherichia coli K12 unable to use fumarate as an anaerobic electron acceptor. J. Gen. Microbiol. 97 145-60 PubMed
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).

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