sodB: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

sodB

Gene Synonym(s)

ECK1652, b1656, JW1648[1], JW1648

Product Desc.

SodB[2][3];

Component of superoxide dismutase (Fe)[2][3]

Superoxide dismutase, Fe; response to oxidative stress; chromate resistance; negatively regulated by ryhB RNA as part of indirect positive regulation by Fur; acid-inducible[4]

Product Synonyms(s)

superoxide dismutase, Fe[1], B1656[2][1], SodB[2][1] , ECK1652, JW1648, b1656

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sodB[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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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

sodB

Mnemonic

SuperOxide Dismutase

Synonyms

ECK1652, b1656, JW1648[1], JW1648

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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

37.36 minutes 

MG1655: 1733402..1733983
<gbrowseImage> name=NC_000913:1733402..1733983 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1712572..1713153
<gbrowseImage> name=NC_012967:1712572..1713153 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1625461..1626042
<gbrowseImage> name=NC_012759:1625461..1626042 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1737092..1737673
<gbrowseImage> name=NC_007779:1737092..1737673 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1823973..1824554
<gbrowseImage> name=NC_010473:1823973..1824554 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

1733405

Edman degradation

PMID:2447093
PMID:3305077
PMID:4590170
PMID:9298646
PMID:9600841
PMID:9740056


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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

ΔsodB (Keio:JW1648)

deletion

deletion

PMID:16738554

Shigen
CGSC9402[5]

sodB::Tn5KAN-I-SceI (FB20409)

Insertion at nt 343 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20409

contains pKD46

ΔsodB734::kan

PMID:16738554

CGSC:102980


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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

JW1648

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCATTCGAATTACCTGCACT

Primer 2:CCTGCAGCGAGATTTTTCGCTAC

6F11

Kohara Phage

Genobase

PMID:3038334

4H6

Kohara Phage

Genobase

PMID:3038334

13H4

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 15% [6]
Synonyms:zdh-925::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:EG10954

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10954

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000943

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944953

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0947

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005537

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

SodB

Synonyms

superoxide dismutase, Fe[1], B1656[2][1], SodB[2][1] , ECK1652, JW1648, b1656

Product description

SodB[2][3];

Component of superoxide dismutase (Fe)[2][3]

Superoxide dismutase, Fe; response to oxidative stress; chromate resistance; negatively regulated by ryhB RNA as part of indirect positive regulation by Fur; acid-inducible[4]

EC number (for enzymes)
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Notes

Paraquat (methyl viologen) & plumbagin generate superoxide.

6-phosphogluconate dehydratase, dihydroxyacid dehydratase, quinolinate synthase, and aconitase are considered to be superoxide sensitive enzymes[7] [8] [9] [10].

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:0004784

superoxide dismutase activity

PMID:4352182

IDA: Inferred from Direct Assay

F

complete

GO:0005737

cytoplasm

PMID:330499

IDA: Inferred from Direct Assay

C

Although SodB was previously localized to the periplasmic space, this was shown to be incorrect by the methods used in this paper (spheroplast formation, osmotic shock & addition of diazo-NDS, an inhibitory reagent that cannot cross the inner membrane).

complete

GO:0004784

superoxide dismutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001189

F

Seeded from EcoCyc (v14.0)

complete

GO:0005506

iron ion binding

PMID:11669646

IPI: Inferred from Physical Interaction

F

Missing: with/from

GO:0004784

superoxide dismutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019831

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

PMID:11669646

IPI: Inferred from Physical Interaction

F

Missing: with/from

GO:0004784

superoxide dismutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019832

F

Seeded from EcoCyc (v14.0)

complete

GO:0004784

superoxide dismutase activity

PMID:1447175

IDA: Inferred from Direct Assay

F

complete

GO:0004784

superoxide dismutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019833

F

Seeded from EcoCyc (v14.0)

complete

GO:0000303

response to superoxide

PMID:1447175

IDA: Inferred from Direct Assay

P

complete

GO:0004784

superoxide dismutase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.15.1.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

PMID:1447175

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:0006801

superoxide metabolic process

PMID:1447175

IDA: Inferred from Direct Assay

P

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

PMID:1447175

IDA: Inferred from Direct Assay

P

complete

GO:0006801

superoxide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001189

P

Seeded from EcoCyc (v14.0)

complete

GO:0019430

removal of superoxide radicals

PMID:1447175

IDA: Inferred from Direct Assay

P

complete

GO:0006801

superoxide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019831

P

Seeded from EcoCyc (v14.0)

complete

GO:0000303

response to superoxide

PMID:3022287

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006801

superoxide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019832

P

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0004784

superoxide dismutase activity

PMID:3022287

IMP: Inferred from Mutant Phenotype

F

complete

GO:0006801

superoxide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019833

P

Seeded from EcoCyc (v14.0)

complete

GO:0006801

superoxide metabolic process

PMID:3022287

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001189

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019831

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019832

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019833

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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

Subunits of superoxide dismutase (Fe)

could be indirect

Protein

evgA

PMID:16606699

Experiment(s):EBI-1140393

Protein

ygaE

PMID:16606699

Experiment(s):EBI-1140393

Protein

rplB

PMID:16606699

Experiment(s):EBI-1140393

Protein

slyD

PMID:16606699

Experiment(s):EBI-1140393

Protein

pal

PMID:16606699

Experiment(s):EBI-1140393

Protein

Fur

sodB is positively regulated by Fur

11917098


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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 

MSFELPALPY AKDALAPHIS AETIEYHYGK HHQTYVTNLN NLIKGTAFEG KSLEEIIRSS
EGGVFNNAAQ VWNHTFYWNC LAPNAGGEPT GKVAEAIAAS FGSFADFKAQ FTDAAIKNFG
SGWTWLVKNS DGKLAIVSTS NAGTPLTTDA TPLLTVDVWE HAYYIDYRNA RPGYLEHFWA
LVNWEFVAKN LAA
Length

193

Mol. Wt

21.265 kDa

pI

5.9 (calculated)

Extinction coefficient

51,910 - 52,035 (calc based on 9 Y, 7 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

Initiator Methionine

1

Removed

UniProt:P0AGD3

Domain

2..82

PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain

PMID:19920124

Domain

87..191

PF02777 Iron/manganese superoxide dismutases, C-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=sodB 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:16129614

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944953

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005537

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGD3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10954

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10954

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944953

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000943

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0947

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

5.85E+03

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 EMG2

2020

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M36

PMID: 9298646

Protein

E. coli K-12 MG1655

33494

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

15086

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

20640

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)

sodB

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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_000913:1733382..1733422 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:b1656 (EcoliWiki Page)

NCBI GEO profiles for sodB

microarray

GenExpDB:b1656 (EcoliWiki Page)

Summary of data for sodB 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 (1733174..1733479) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:G11[11]

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Notes

Accessions Related to sodB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10954

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0947

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1656

EcoGene

EcoGene:EG10954

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000943

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005537

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

Apis mellifera

  • ENSAPMP00000022865 (score: 1.000; bootstrap: 94%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G51100 (score: 1.000; bootstrap: 96%)
  • AT4G25100 (score: 0.240)
  • AT5G23310 (score: 0.125)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000008569 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000007739 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5FB28 (score: 1.000; bootstrap: 99%)
  • Q5VSB7 (score: 0.734)
  • Q9ZWM8 (score: 0.726)
  • Q4VQ67 (score: 0.340)
  • Q5W1C2 (score: 0.258)
  • Q52WX4 (score: 0.247)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000028824 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

SODB

From SHIGELLACYC

E. coli O157

SODB

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:46609

Panther (EcoliWiki Page)

PTHR11404:SF8

Superfamily (EcoliWiki Page)

SUPERFAMILY:54719

Pfam (EcoliWiki Page)

PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain

Pfam (EcoliWiki Page)

PF02777 Iron/manganese superoxide dismutases, C-terminal domain

EcoCyc

EcoCyc:EG10954

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10954

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000943

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0947

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005537

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 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 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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. ↑ Gardner, PR & Fridovich, I (1991) Superoxide sensitivity of the Escherichia coli 6-phosphogluconate dehydratase. J. Biol. Chem. 266 1478-83 PubMed
  8. ↑ Gardner, PR & Fridovich, I (1991) Superoxide sensitivity of the Escherichia coli aconitase. J. Biol. Chem. 266 19328-33 PubMed
  9. ↑ Gardner, PR & Fridovich, I (1991) Quinolinate synthetase: the oxygen-sensitive site of de novo NAD(P)+ biosynthesis. Arch. Biochem. Biophys. 284 106-11 PubMed
  10. ↑ Kuo, CF et al. (1987) alpha, beta-Dihydroxyisovalerate dehydratase. A superoxide-sensitive enzyme. J. Biol. Chem. 262 4724-7 PubMed
  11. ↑ 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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