acnB: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

acnB

Gene Synonym(s)

ECK0117, b0118, JW0114, yacI, yacJ[1], yacJ

Product Desc.

Aconitase B; 2-methylaconitate hydratase; apo-enzyme binds mRNA for negative translational autoregulation; iron-sulfur cluster; monomeric[2]

Product Synonyms(s)

bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase[1], B0118[3][1], YacI[3][1], YacJ[3][1], AcnB[3][1] , ECK0117, JW0114, yacI, yacJ, b0118

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): acnB[3]

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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Binds TrxA (Kumar, 2004).[2]



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

acnB

Mnemonic

Aconitase

Synonyms

ECK0117, b0118, JW0114, yacI, yacJ[1], yacJ

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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

2.84 minutes 

MG1655: 131615..134212
<gbrowseImage> name=NC_000913:131615..134212 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 134419..137016
<gbrowseImage> name=NC_012967:134419..137016 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 131614..134211
<gbrowseImage> name=NC_012759:131614..134211 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 131615..134212
<gbrowseImage> name=NC_007779:131615..134212 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 105719..108316
<gbrowseImage> name=NC_010473:105719..108316 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

131615

Edman degradation

PMID:8932712
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

acnB(del) (Keio:JW0114)

deletion

deletion

PMID:16738554

Shigen

CGSC8396[4]

acnB(del)::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938

acnB(del)::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938

acnB(del)::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938

acnB(del)::tetR

Internal deletion of acnB replaced with tetR gene.

Growth Phenotype

Cannot grow on acetate as the sole carbon and energy source with or without supplementation with glutamate.

PMID:9202458

acnB(del)::tetR

Internal deletion of acnB substituted with tetR.

Growth Phenotype

Grows poorly on minimal glucose medium unless the medium is supplemented with glutamate. The same phenotype is seen for growth on minimal medium with glycerol, lactate, pyruvate, or succinate as the carbon and energy source.

PMID:9202458

Mutants lacking citrate synthase (gltA) or isocitrate dehydrogenase (icd) are glutamate auxotrophs. The mutant lacking acnB doesn't have an absolutely requirement for glutamate because of the second aconitase activity (acnA).

acnB736(del)::kan

PMID:16738554

CGSC:99896


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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

JW0114

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCTAGAAGAATACCGTAAGCA

Primer 2:CCAACCGCAGTCTGGAAAATCAC

4D12

Kohara Phage

Genobase

PMID:3038334

4E11

Kohara Phage

Genobase

PMID:3038334

17C11

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 11% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[4]

est. P1 cotransduction: 55% [5]

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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:EG12316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002193

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944864

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2222

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000411

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

AcnB

Synonyms

bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase[1], B0118[3][1], YacI[3][1], YacJ[3][1], AcnB[3][1] , ECK0117, JW0114, yacI, yacJ, b0118

Product description

Aconitase B; 2-methylaconitate hydratase; apo-enzyme binds mRNA for negative translational autoregulation; iron-sulfur cluster; monomeric[2]

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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003994

aconitate hydratase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004406

F

Seeded from EcoCyc (v14.0)

complete

GO:0003994

aconitate hydratase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015929

F

Seeded from EcoCyc (v14.0)

complete

GO:0003994

aconitate hydratase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015930

F

Seeded from EcoCyc (v14.0)

complete

GO:0003994

aconitate hydratase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015933

F

Seeded from EcoCyc (v14.0)

complete

GO:0003994

aconitate hydratase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.2.1.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0003994

aconitate hydratase activity

PMID:8932712

IDA: Inferred from Direct Assay

F

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:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004406

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015929

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015933

F

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004406

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015929

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015930

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015933

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0816

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:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004406

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015930

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

GO:0006097

glyoxylate cycle

PMID:10589714

NAS: Non-traceable Author Statement

P

complete

GO:0006099

tricarboxylic acid cycle

PMID:10589714

NAS: Non-traceable Author Statement

P

complete

GO:0003729

mRNA binding

PMID:10589714

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

speD

PMID:16606699

Experiment(s):EBI-1135623, EBI-1135640

Protein

zwf

PMID:16606699

Experiment(s):EBI-1135623

Protein

ulaB

PMID:16606699

Experiment(s):EBI-1135623

Protein

sbcC

PMID:16606699

Experiment(s):EBI-1135623

Protein

groL

PMID:16606699

Experiment(s):EBI-1135623

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6

Protein

dapB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gatA

PMID:19402753

LCMS(ID Probability):99.6

Protein

gcvP

PMID:19402753

LCMS(ID Probability):99.6

Protein

gabD

PMID:19402753

LCMS(ID Probability):99.6

Protein

php

PMID:19402753

LCMS(ID Probability):99.4

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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 

MLEEYRKHVA ERAAEGIAPK PLDANQMAAL VELLKNPPAG EEEFLLDLLT NRVPPGVDEA
AYVKAGFLAA IAKGEAKSPL LTPEKAIELL GTMQGGYNIH PLIDALDDAK LAPIAAKALS
HTLLMFDNFY DVEEKAKAGN EYAKQVMQSW ADAEWFLNRP ALAEKLTVTV FKVTGETNTD
DLSPAPDAWS RPDIPLHALA MLKNAREGIE PDQPGVVGPI KQIEALQQKG FPLAYVGDVV
GTGSSRKSAT NSVLWFMGDD IPHVPNKRGG GLCLGGKIAP IFFNTMEDAG ALPIEVDVSN
LNMGDVIDVY PYKGEVRNHE TGELLATFEL KTDVLIDEVR AGGRIPLIIG RGLTTKAREA
LGLPHSDVFR QAKDVAESDR GFSLAQKMVG RACGVKGIRP GAYCEPKMTS VGSQDTTGPM
TRDELKDLAC LGFSADLVMQ SFCHTAAYPK PVDVNTHHTL PDFIMNRGGV SLRPGDGVIH
SWLNRMLLPD TVGTGGDSHT RFPIGISFPA GSGLVAFAAA TGVMPLDMPE SVLVRFKGKM
QPGITLRDLV HAIPLYAIKQ GLLTVEKKGK KNIFSGRILE IEGLPDLKVE QAFELTDASA
ERSAAGCTIK LNKEPIIEYL NSNIVLLKWM IAEGYGDRRT LERRIQGMEK WLANPELLEA
DADAEYAAVI DIDLADIKEP ILCAPNDPDD ARPLSAVQGE KIDEVFIGSC MTNIGHFRAA
GKLLDAHKGQ LPTRLWVAPP TRMDAAQLTE EGYYSVFGKS GARIEIPGCS LCMGNQARVA
DGATVVSTST RNFPNRLGTG ANVFLASAEL AAVAALIGKL PTPEEYQTYV AQVDKTAVDT
YRYLNFNQLS QYTEKADGVI FQTAV
Length

865

Mol. Wt

93.5 kDa

pI

5.2 (calculated)

Extinction coefficient

75,290 - 76,540 (calc based on 21 Y, 8 W, and 10 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

Modification Site

242

phosphorylation site at T242

probability less than 75%

PMID:17938405

Modification Site

622

phosphorylation site at S622

probability greater than 75%

PMID:17938405

Modification Site

245

phosphorylation site at S245

probability less than 75%

PMID:17938405

Modification Site

242

phosphorylation site at T242

probability less than 75%

PMID:17938405

Domain

464..701

PF00330 Aconitase family (aconitate hydratase)

PMID:19920124

Domain

695..818

PF00330 Aconitase family (aconitate hydratase)

PMID:19920124

Domain

168..382

PF06434 Aconitate hydratase 2 N-terminus

PMID:19920124

Domain

4..156

PF11791 Aconitate B N-terminal 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=acnB 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:16128111

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944864

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000411

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P36683

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12316

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944864

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002193

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2222

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

231.593+/-2.098

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.05933+/-0.00822

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.436657682

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

7764

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

7660

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

6068

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)

acnB

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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_000913:131595..131635 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:b0118 (EcoliWiki Page)

NCBI GEO profiles for acnB

microarray

GenExpDB:b0118 (EcoliWiki Page)

Summary of data for acnB 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 (131187..131681) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ02; Well:H10[6]

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Notes

Accessions Related to acnB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12316

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2222

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0118

EcoGene

EcoGene:EG12316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002193

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000411

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

Xenopus tropicalis

  • ENSXETP00000047983 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

ACNB

From SHIGELLACYC

E. coli O157

ACNB

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)

PF00330 Aconitase family (aconitate hydratase)

Pfam (EcoliWiki Page)

PF00330 Aconitase family (aconitate hydratase)

Superfamily (EcoliWiki Page)

SUPERFAMILY:52016

Panther (EcoliWiki Page)

PTHR11670:SF3

Superfamily (EcoliWiki Page)

SUPERFAMILY:53732

Superfamily (EcoliWiki Page)

SUPERFAMILY:74778

Pfam (EcoliWiki Page)

PF06434 Aconitate hydratase 2 N-terminus

Pfam (EcoliWiki Page)

PF11791 Aconitate B N-terminal domain

EcoCyc

EcoCyc:EG12316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002193

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2222

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000411

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 1.12 1.13 1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ 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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