uvrY:On One Page

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

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Standard Name

uvrY

Gene Synonym(s)

ECK1913, b1914, JW1899, yecB[1], gacA, sirA, yecB

Product Desc.

UvrY transcriptional regulator[2][3]

Response regulator, pleiotrpic; controls the expression of csrB/C sRNAs; hydrogen peroxide resistance; cognate sensorregulator is BarA[4]

Product Synonyms(s)

DNA-binding response regulator in two-component regulatory system with BarA [1], YecB [2][1], B1914 [2][1], UvrY-Pasp [2][1] , ECK1913, gacA, JW1899, sirA, yecB, b1914

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): uvrYC[2]

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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Salmonella ortholog regulates virulence gene expression.[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

uvrY

Mnemonic

UV resistant

Synonyms

ECK1913, b1914, JW1899, yecB[1], gacA, sirA, yecB

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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

42.95 minutes 

MG1655: 1993383..1992727
<gbrowseImage> name=NC_000913:1992727..1993383 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1973205..1972696
<gbrowseImage> name=NC_012967:1972696..1973205 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1885210..1885866
<gbrowseImage> name=NC_012759:1885210..1885866 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1997496..1996840
<gbrowseImage> name=NC_007779:1996840..1997496 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2084391..2083735
<gbrowseImage> name=NC_010473:2083735..2084391 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
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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

uvrY(del) (Keio:JW1899)

deletion

deletion

PMID:16738554

Shigen

CGSC9580[5]

uvrY1310(del)

PMID:12897016

CGSC:82175

uvrY1362(del)

CGSC:82180

uvrY1296(del)

PMID:12366850

CGSC:89616

uvrY760(del)::kan

PMID:16738554

CGSC:103350

uvrY760(del)::FRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554

Parental Strain: SMR4562

Experimental Strain: SMR12314

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

uvrY760(del)::FRT

Sensitivity to

An increase in UV Sensitivity. Supplemental Table S7 & S1.

PMID:23224554

Parental Strain: SMR4562

Experimental Strain: SMR12050

See Table S1 & S7

SMR6039 uvrY760(del)::FRTkanFRT

deletion

SOS response

Decrease in spontaneous SOS-induction defective.

PMID:23224554

Parental Strain: SMR6039

Experimental Strain: SMR15980

See table S7 for a summary of experimental results.

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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

JW1899

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCAACGTTCTACTTGTTGA

Primer 2:CCtTGACTTGATAATGTCTCCGC

16B12

Kohara Phage

Genobase

PMID:3038334

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 93% [6]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[5]

est. P1 cotransduction: 14% [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:EG11140

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11140

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001124

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946424

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1130

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006373

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

UvrY

Synonyms

DNA-binding response regulator in two-component regulatory system with BarA [1], YecB [2][1], B1914 [2][1], UvrY-Pasp [2][1] , ECK1913, gacA, JW1899, sirA, yecB, b1914

Product description

UvrY transcriptional regulator[2][3]

Response regulator, pleiotrpic; controls the expression of csrB/C sRNAs; hydrogen peroxide resistance; cognate sensorregulator is BarA[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:0000156

two-component response regulator activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

F

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

P

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0902

P

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:IPR000792

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000792

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:IPR000792

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:IPR001789

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000792

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

lpdA

PMID:15690043

Experiment(s):EBI-880857

Protein

tufA

PMID:15690043

Experiment(s):EBI-880857

Protein

hscC

PMID:15690043

Experiment(s):EBI-887064

Protein

fimZ

PMID:15690043

Experiment(s):EBI-887064

Protein

rplL

PMID:15690043

Experiment(s):EBI-887064

Protein

yghW

PMID:16606699

Experiment(s):EBI-1141304

Protein

rpsM

PMID:16606699

Experiment(s):EBI-1141304

Protein

narX

PMID:16606699

Experiment(s):EBI-1141304

Protein

ahpF

PMID:16606699

Experiment(s):EBI-1141304

Protein

yciH

PMID:16606699

Experiment(s):EBI-1141304

Protein

murB

PMID:16606699

Experiment(s):EBI-1141304

Protein

nagZ

PMID:16606699

Experiment(s):EBI-1141304

Protein

tufB

PMID:19402753

MALDI(Z-score):18.715338

Protein

hscC

PMID:19402753

LCMS(ID Probability):99.6

Protein

fimZ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

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
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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 

MINVLLVDDH ELVRAGIRRI LEDIKGIKVV GEASCGEDAV KWCRTNAVDV VLMDMSMPGI
GGLEATRKIA RSTADVKIIM LTVHTENPLP AKVMQAGAAG YLSKGAAPQE VVSAIRSVYS
GQRYIASDIA QQMALSQIEP EKTESPFASL SERELQIMLM ITKGQKVNEI SEQLNLSPKT
VNSYRYRMFS KLNIHGDVEL THLAIRHGLC NAETLSSQ
Length

218

Mol. Wt

23.892 kDa

pI

7.0 (calculated)

Extinction coefficient

12,950 - 13,325 (calc based on 5 Y, 1 W, and 3 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

147..204

PF00196 Bacterial regulatory proteins, luxR family

PMID:19920124

Domain

4..116

PF00072 Response regulator receiver domain

PMID:19920124

Modification Site

Phosphorylation

phosphorylated by BarA

PMID:11022030

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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=uvrY 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:16129861

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946424

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006373

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AED5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11140

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11140

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946424

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001124

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1130

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

29.111+/-0.225

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.138719512

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

880

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

412

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

722

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)

uvrYC

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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_000913:1993363..1993403 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:b1914 (EcoliWiki Page)

NCBI GEO profiles for uvrY

microarray

GenExpDB:b1914 (EcoliWiki Page)

Summary of data for uvrY 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 (1993282..1993900) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:C6[7]

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Notes

Accessions Related to uvrY Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11140

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1130

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1914

EcoGene

EcoGene:EG11140

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001124

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006373

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Arabidopsis thaliana

  • AT5G62920 (score: 1.000; bootstrap: 100%)
  • AT3G48100 (score: 0.735)
  • AT2G41310 (score: 0.379)
  • AT3G57040 (score: 0.369)
  • AT2G40670 (score: 0.346)
  • AT3G56380 (score: 0.337)
  • AT2G46790 (score: 0.065)
  • AT2G07440 (score: 0.061)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000012539 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Shigella flexneri

UVRY

From SHIGELLACYC

E. coli O157

UVRY

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)

PF00196 Bacterial regulatory proteins, luxR family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46894

Superfamily (EcoliWiki Page)

SUPERFAMILY:52172

Panther (EcoliWiki Page)

PTHR24423:SF376

Pfam (EcoliWiki Page)

PF00072 Response regulator receiver domain

EcoCyc

EcoCyc:EG11140

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11140

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001124

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1130

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006373

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 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 5.2 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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