uspF:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

uspF

Gene Synonym(s)

ECK1371, b1376, JW1370, ynaF, yzzL, up03[1]

Product Desc.

nucleotide binding protein[2]; nucleotide binding filament protein[3]

Stress-induced protein, binds ATP; dimer[4]

Product Synonyms(s)

stress-induced protein, ATP-binding protein[1], B1376[2][1], YzzL[2][1], UspF[2][1], YnaF[2][1] , ECK1371, JW1370, ynaF, yzzL, b1376

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): uspF[2]

Regulation/Activity
Quick Links



        

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Notes

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NMR solution structure determined for E. coli UspF(YnaF) (Saveanu, 2002). otherPDB (M. jannaschii): 1MJH.[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

uspF

Mnemonic

Universal stress protein

Synonyms

ECK1371, b1376, JW1370, ynaF, yzzL, up03[1]

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Notes

Location(s) and DNA Sequence

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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

30.89 minutes 

MG1655: 1433643..1433209
<gbrowseImage> name=NC_000913:1433209..1433643 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1325268..1325702
<gbrowseImage> name=NC_012759:1325268..1325702 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1437333..1436899
<gbrowseImage> name=NC_007779:1436899..1437333 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1524238..1523804
<gbrowseImage> name=NC_010473:1523804..1524238 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

1433209

Edman degradation

PMID:8740179
PMID:9298646


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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

ΔuspF (Keio:JW1370)

deletion

deletion

PMID:16738554

Shigen

ΔyzzL::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938


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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

JW1370

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACAGAACGATTCTTGTCCC

Primer 2:CCGCGCACAACCAGCACGGAGCA

4E7

Kohara Phage

Genobase

PMID:3038334

1E7

Kohara Phage

Genobase

PMID:3038334

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[5]

est. P1 cotransduction: 43% [6]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[5]

est. P1 cotransduction: 99% [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:G6699

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12674

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003294

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945948

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2539

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004605

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

UspF

Synonyms

stress-induced protein, ATP-binding protein[1], B1376[2][1], YzzL[2][1], UspF[2][1], YnaF[2][1] , ECK1371, JW1370, ynaF, yzzL, b1376

Product description

nucleotide binding protein[2]; nucleotide binding filament protein[3]

Stress-induced protein, binds ATP; dimer[4]

EC number (for enzymes)


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Notes

Function

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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:0006950

response to stress

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006016

P

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:12381839[7]

IDA: Inferred from Direct Assay

F

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

rplO

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

ssuE

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rplD

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

dnaK

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

paaB

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

yfjM

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rpsM

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

hflK

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rplE

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rluC

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

ycgL

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

nadE

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

matC

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rplS

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

ybaO

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

intB

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

secB

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rpsI

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

cybC

PMID:16606699[8]

Experiment(s):EBI-1139703

Protein

rplS

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

secA

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

yohF

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

lptB

PMID:19402753[9]

LCMS(ID Probability):99.4

Protein

argS

PMID:19402753[9]

LCMS(ID Probability):99.6

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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

PMID:8391533

EchoLocation:uspF


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Notes

Structure and Physical Properties

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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 

MNSVITQKVS SGVTLYADTK TGGFMNRTIL VPIDISDSEL TQRVISHVEE EAKIDDAEVH
FLTVIPSLPY YASLGLAYSA ELPAMDDLKA EAKSQLEEII KKFKLPTDRV HVHVEEGSPK
DRILELAKKI PAHMIIIASH RPDITTYLLG SNAAAVVRHA ECSVLVVR
Length

168

Mol. Wt

18.503 kDa

pI

6.2 (calculated)

Extinction coefficient

7,450 - 7,575 (calc based on 5 Y, 0 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 Notes References

Domain

1..144

PF00582 Universal stress protein family

PMID:19920124[10]

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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=uspF taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:90111262

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945948

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004605

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P37903

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6699

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12674

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945948

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003294

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2539

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

Ecoli K-12

125.83+/-0.999

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.39359+/-0.07692

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

Protein

E. coli K-12 MG1655

189

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

633

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

176

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)

uspF

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Figure courtesy of RegulonDB


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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<gbrowseImage> name=NC_000913:1433623..1433663 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


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

</protect>

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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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:b1376 (EcoliWiki Page)

NCBI GEO profiles for uspF

microarray

GenExpDB:b1376 (EcoliWiki Page)

Summary of data for uspF 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 (1433615..1433836) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ16; Well:B7[11]

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<protect>

Notes

Accessions Related to uspF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6699

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2539

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1376

EcoGene

EcoGene:EG12674

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003294

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004605

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

Shigella flexneri

YNAF

From SHIGELLACYC

E. coli O157

YNAF

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:52402

Pfam (EcoliWiki Page)

PF00582 Universal stress protein family

EcoCyc

EcoCyc:G6699

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12674

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003294

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2539

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004605

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Saveanu, C et al. (2002) Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function. Protein Sci. 11 2551-60 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.0 9.1 9.2 9.3 9.4 9.5 9.6 9.7 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
  11. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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