atoC: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

atoC

Gene Synonym(s)

ECK2213, b2220, JW2214, Az[1], Az

Product Desc.

Response regulator for atoDAEB operon[2]

Response regulator for atoDAEB operon; AtoS is the two-component cognate sensor protein; induced by acetoacetate; ornithine decarboxylase antizyme Az, polyamine-inducible[3]

Product Synonyms(s)

B2220[4][1], Az, ECK2213, JW2214, b2220

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): atoS[4]

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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Bifunctional bacterial antizyme AtoC(Az) binds to and inhibits ornithine decarboxylase. AtoCS mutants have lowered complexed poly-(R)-3-hydroxybutyrate (cPHB) levels: the ato operon is required for maximal cPHB production (Theodoroua, 2006).[3]



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

atoC

Mnemonic

Acetoacetate

Synonyms

ECK2213, b2220, JW2214, Az[1], Az

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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

50 minutes 

MG1655: 2319888..2321273
<gbrowseImage> name=NC_000913:2319888..2321273 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2268566..2269951
<gbrowseImage> name=NC_012967:2268566..2269951 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2205693..2207078
<gbrowseImage> name=NC_012759:2205693..2207078 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2326536..2327921
<gbrowseImage> name=NC_007779:2326536..2327921 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2410876..2412261
<gbrowseImage> name=NC_010473:2410876..2412261 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

atoC(del) (Keio:JW2214)

deletion

deletion

PMID:16738554

Shigen
CGSC9785[5]

atoC12

PMID:353047

CGSC:7257

atoC200(Const)

constitutive

CGSC:7482

atoC512(Const)

constitutive

CGSC:16174

atoC531

CGSC:17103

atoC561

CGSC:17105

atoC774(del)::kan

PMID:16738554

CGSC:100126


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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

JW2214

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTGCTATTAATCGCATCCT

Primer 2:CCTACATCCGCCGGATCGATACC

5A1

Kohara Phage

Genobase

PMID:3038334

4F12

Kohara Phage

Genobase

PMID:3038334

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[5]

est. P1 cotransduction: 100% [6]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[5]

est. P1 cotransduction: 42% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

mutants

Strain

PMID:2883171

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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:EG11668

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11668

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001611

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947444

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1619

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007343

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

AtoC

Synonyms

B2220[4][1], Az, ECK2213, JW2214, b2220

Product description

Response regulator for atoDAEB operon[2]

Response regulator for atoDAEB operon; AtoS is the two-component cognate sensor protein; induced by acetoacetate; ornithine decarboxylase antizyme Az, polyamine-inducible[3]

EC number (for enzymes)


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Notes

AtoS is the two-component cognate sensor protein for AtoC; induced by acetoacetate; ornithine decarboxylase antizyme Az, polyamine-inducible[2]

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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002197

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020441

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:2883171

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:8346225

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P03029
UniProtKB:P13632
UniProtKB:P06519
UniProtKB:P05407
UniProtKB:P17899
UniProtKB:P14375

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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:0008134

transcription factor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:2883171

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:8346225

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P03029
UniProtKB:P13632
UniProtKB:P06519
UniProtKB:P05407
UniProtKB:P17899
UniProtKB:P14375

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:2883171

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:8346225

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P03029
UniProtKB:P13632
UniProtKB:P06519
UniProtKB:P05407
UniProtKB:P17899
UniProtKB:P14375

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

rpsD

PMID:16606699

Experiment(s):EBI-1142209

Protein

rpsL

PMID:16606699

Experiment(s):EBI-1142209

Protein

nadE

PMID:16606699

Experiment(s):EBI-1142209

Protein

rplS

PMID:16606699

Experiment(s):EBI-1142209

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1142209

Protein

ydbC

PMID:16606699

Experiment(s):EBI-1142209

Protein

rplO

PMID:16606699

Experiment(s):EBI-1142209
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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[7]


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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 

MTAINRILIV DDEDNVRRML STAFALQGFE THCANNGRTA LHLFADIHPD VVLMDIRMPE
MDGIKALKEM RSHETRTPVI LMTAYAEVET AVEALRCGAF DYVIKPFDLD ELNLIVQRAL
QLQSMKKEIR HLHQALSTSW QWGHILTNSP AMMDICKDTA KIALSQASVL ISGESGTGKE
LIARAIHYNS RRAKGPFIKV NCAALPESLL ESELFGHEKG AFTGAQTLRQ GLFERANEGT
LLLDEIGEMP LVLQAKLLRI LQEREFERIG GHQTIKVDIR IIAATNRDLQ AMVKEGTFRE
DLFYRLNVIH LILPPLRDRR EDISLLANHF LQKFSSENQR DIIDIDPMAM SLLTAWSWPG
NIRELSNVIE RAVVMNSGPI IFSEDLPPQI RQPVCNAGEV KTAPVGERNL KEEIKRVEKR
IIMEVLEQQE GNRTRTALML GISRRALMYK LQEYGIDPAD V
Length

461

Mol. Wt

52.177 kDa

pI

6.4 (calculated)

Extinction coefficient

30,940 - 31,565 (calc based on 6 Y, 4 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

413..454

PF02954 Bacterial regulatory protein, Fis family

PMID:19920124

Domain

7..117

PF00072 Response regulator receiver domain

PMID:19920124

Domain

145..312

PF00158 Sigma-54 interaction 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=atoC 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:16130157

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947444

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007343

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q06065

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11668

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11668

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947444

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001611

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1619

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 MG1655

42

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

32

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

15a

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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<protect>

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

Transcription unit(s)

atoS

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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_000913:2319868..2319908 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:b2220 (EcoliWiki Page)

NCBI GEO profiles for atoC

microarray

GenExpDB:b2220 (EcoliWiki Page)

Summary of data for atoC 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 atoC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11668

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1619

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2220

EcoGene

EcoGene:EG11668

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001611

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007343

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

  • AT1G19050 (score: 1.000; bootstrap: 100%)
  • AT1G74890 (score: 0.581)
  • AT5G24470 (score: 0.061)
  • AT5G02810 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q4GZL0 (score: 1.000; bootstrap: 100%)
  • Q9FRY8 (score: 0.455)
  • Q6YVX7 (score: 0.448)
  • Q4GZK9 (score: 0.448)
  • Q7XRI1 (score: 0.361)
  • Q6H468 (score: 0.164)
  • Q9FRZ0 (score: 0.159)
  • Q9FXQ7 (score: 0.157)
  • Q7XKF6 (score: 0.157)
  • Q4GZK6 (score: 0.152)
  • Q942A1 (score: 0.152)
  • Q4GZK7 (score: 0.152)
  • Q9FRZ1 (score: 0.147)
  • Q6K9T0 (score: 0.144)
  • Q4GZK8 (score: 0.144)
  • Q4GZK2 (score: 0.137)
  • Q9FRY9 (score: 0.134)
  • Q9S7U8 (score: 0.134)
  • Q7XQA6 (score: 0.134)
  • Q4JF20 (score: 0.134)
  • Q4GZK5 (score: 0.134)
  • Q8H5N4 (score: 0.122)
  • Q4GZK4 (score: 0.122)
  • Q9ZQW0 (score: 0.117)
  • Q8GVV6 (score: 0.092)
  • Q4GZK3 (score: 0.092)
  • Q8GVV1 (score: 0.055)
  • Q6YZK8 (score: 0.055)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000032313 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

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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)

PF02954 Bacterial regulatory protein, Fis family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:52172

Panther (EcoliWiki Page)

PTHR24423:SF442

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF00072 Response regulator receiver domain

Pfam (EcoliWiki Page)

PF00158 Sigma-54 interaction domain

EcoCyc

EcoCyc:EG11668

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11668

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001611

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1619

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007343

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2
  3. ↑ 3.0 3.1 3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.0 4.1 4.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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