sodA: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

sodA

Gene Synonym(s)

ECK3901, b3908, JW3879[1], JW3879

Product Desc.

SodA[2][3];

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

Superoxide dismutase, Mn[4]

Product Synonyms(s)

superoxide dismutase, Mn[1], B3908[2][1], SodA[2][1] , ECK3901, JW3879, b3908

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sodA[2], OP00089

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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SoxRS regulon. Binds TrxA (Kumar, 2004).[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

sodA

Mnemonic

SuperOxide Dismutase

Synonyms

ECK3901, b3908, JW3879[1], JW3879

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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

88.34 minutes, 88.34 minutes 

MG1655: 4098833..4099453
<gbrowseImage> name=NC_000913:4098833..4099453 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4080292..4080912
<gbrowseImage> name=NC_012967:4080292..4080912 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3988502..3989122
<gbrowseImage> name=NC_012759:3988502..3989122 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3535871..3535251
<gbrowseImage> name=NC_007779:3535251..3535871 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4198530..4199150
<gbrowseImage> name=NC_010473:4198530..4199150 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

4098836

Edman degradation

PMID:363708
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

ΔsodA (Keio:JW3879)

deletion

deletion

PMID:16738554

Shigen
CGSC10798[5]

sodAM165L

M165L

(in strain: B)

Strain variation; seeded from UniProt:P00448

sodA25::MudPR13

CGSC:26963

ΔsodA768::kan

PMID:16738554

CGSC:102978


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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

JW3879

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCTATACCCTGCCATCCCT

Primer 2:CCTTTTTTCGCCGCAAAACGTGC

4B6

Kohara Phage

Genobase

PMID:3038334

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[5]

est. P1 cotransduction: 25% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 14% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG10953

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10953

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000942

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948403

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0946

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012761

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

SodA

Synonyms

superoxide dismutase, Mn[1], B3908[2][1], SodA[2][1] , ECK3901, JW3879, b3908

Product description

SodA[2][3];

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

Superoxide dismutase, Mn[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:0004784

superoxide dismutase activity

PMID:4921969

IDA: Inferred from Direct Assay

F

complete

GO:0019430

removal of superoxide radicals

PMID:4943714

IDA: Inferred from Direct Assay

P

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:0055114

oxidation reduction

PMID:4943714

IDA: Inferred from Direct Assay

P

complete

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:0005737

cytoplasm

PMID:4580575

IDA: Inferred from Direct Assay

C

complete

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:0046872

metal ion binding

PMID:4921969

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:0006801

superoxide metabolic process

PMID:4196244

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:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001189

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019831

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019832

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019833

F

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: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 (Mn)

could be indirect

Protein

intS

PMID:16606699

Experiment(s):EBI-1146986

Protein

yicC

PMID:16606699

Experiment(s):EBI-1146986

Protein

alr

PMID:16606699

Experiment(s):EBI-1146986

Protein

atoA

PMID:16606699

Experiment(s):EBI-1146986

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1146986

Protein

glpC

PMID:16606699

Experiment(s):EBI-1146986
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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 

MSYTLPSLPY AYDALEPHFD KQTMEIHHTK HHQTYVNNAN AALESLPEFA NLPVEELITK
LDQLPADKKT VLRNNAGGHA NHSLFWKGLK KGTTLQGDLK AAIERDFGSV DNFKAEFEKA
AASRFGSGWA WLVLKGDKLA VVSTANQDSP LMGEAISGAS GFPIMGLDVW EHAYYLKFQN
RRPDYIKEFW NVVNWDEAAA RFAAKK
Length

206

Mol. Wt

23.097 kDa

pI

7.0 (calculated)

Extinction coefficient

43,430 (calc based on 7 Y, 6 W, and 0 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:P00448

Domain

2..90

PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain

PMID:19920124

Domain

93..202

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=sodA 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:49176442

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948403

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012761

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00448

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10953

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10953

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948403

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000942

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0946

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

3.69E+04

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

2980

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: M38�1

PMID: 9298646

Protein

E. coli K-12 MG1655

50220

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

20479

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

20982

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)

sodA

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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_000913:4098813..4098853 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:b3908 (EcoliWiki Page)

NCBI GEO profiles for sodA

microarray

GenExpDB:b3908 (EcoliWiki Page)

Summary of data for sodA 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 (4098032..4098468) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:E11[7]

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Notes

Accessions Related to sodA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10953

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0946

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3908

EcoGene

EcoGene:EG10953

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000942

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012761

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

Anopheles gambiae

  • ENSANGP00000020588 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

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

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00033632 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00004931 (score: 1.000; bootstrap: 100%)
  • WBGene00004932 (score: 0.814)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000000951 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000008809 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030131-7742 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-869 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0202901 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0010213 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21401-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000019039 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000351054 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

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

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000009333 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:98352 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • P93606 (score: 1.000; bootstrap: 99%)
  • Q96185 (score: 0.968)
  • Q56DH8 (score: 0.965)
  • O82571 (score: 0.890)
  • P09233 (score: 0.813)
  • Q43273 (score: 0.810)
  • P41980 (score: 0.800)
  • Q7GCN0 (score: 0.787)
  • Q43121 (score: 0.787)
  • Q43803 (score: 0.781)
  • Q43008 (score: 0.777)
  • P41979 (score: 0.761)
  • P41978 (score: 0.755)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000032013 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000025794 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YHR008C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC14861 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000152842 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00023108001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000045789 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

SODA

From SHIGELLACYC

E. coli O157

SODA

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:SF9

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:EG10953

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10953

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000942

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0946

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012761

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 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

Categories

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