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Protein

Superoxide dismutase [Fe]

Gene

sodB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.

Catalytic activityi

2 superoxide + 2 H+ = O2 + H2O2.1 Publication

Cofactori

Fe cation1 PublicationNote: Binds 1 Fe cation per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi27 – 271Iron
Metal bindingi74 – 741Iron
Metal bindingi157 – 1571Iron
Metal bindingi161 – 1611Iron

GO - Molecular functioni

  1. iron ion binding Source: EcoCyc
  2. oxidoreductase activity Source: EcoliWiki
  3. superoxide dismutase activity Source: EcoliWiki

GO - Biological processi

  1. oxidation-reduction process Source: EcoliWiki
  2. removal of superoxide radicals Source: EcoliWiki
  3. response to superoxide Source: EcoliWiki
  4. superoxide metabolic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:SUPEROX-DISMUTFE-MONOMER.
ECOL316407:JW1648-MONOMER.
MetaCyc:SUPEROX-DISMUTFE-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Superoxide dismutase [Fe] (EC:1.15.1.1)
Gene namesi
Name:sodB
Ordered Locus Names:b1656, JW1648
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10954. sodB.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: EcoliWiki
  2. cytosol Source: UniProtKB
  3. membrane Source: UniProtKB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed3 Publications
Chaini2 – 193192Superoxide dismutase [Fe]PRO_0000159979Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei51 – 511N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0AGD3.
PRIDEiP0AGD3.

2D gel databases

SWISS-2DPAGEP0AGD3.

Expressioni

Gene expression databases

GenevestigatoriP0AGD3.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

IntActiP0AGD3. 6 interactions.
STRINGi511145.b1656.

Structurei

Secondary structure

1
193
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni12 – 187Combined sources
Helixi21 – 299Combined sources
Helixi31 – 4313Combined sources
Turni47 – 504Combined sources
Helixi53 – 575Combined sources
Helixi62 – 7918Combined sources
Helixi91 – 10111Combined sources
Helixi104 – 11714Combined sources
Beta strandi120 – 1289Combined sources
Beta strandi134 – 1407Combined sources
Helixi145 – 1473Combined sources
Beta strandi151 – 1577Combined sources
Helixi160 – 1623Combined sources
Helixi164 – 1674Combined sources
Helixi171 – 1799Combined sources
Helixi184 – 1929Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ISAX-ray1.80A/B2-193[»]
1ISBX-ray1.85A/B2-193[»]
1ISCX-ray1.80A/B2-193[»]
1ZA5X-ray1.80A/B2-193[»]
2BKBX-ray1.70A/B/C/D2-193[»]
2NYBX-ray1.10A/B/C/D2-193[»]
ProteinModelPortaliP0AGD3.
SMRiP0AGD3. Positions 2-193.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGD3.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0605.
HOGENOMiHOG000013584.
InParanoidiP0AGD3.
KOiK04564.
OMAiGGGNKLP.
OrthoDBiEOG63NMNT.
PhylomeDBiP0AGD3.

Family and domain databases

InterProiIPR001189. Mn/Fe_SOD.
IPR019833. Mn/Fe_SOD_BS.
IPR019832. Mn/Fe_SOD_C.
IPR019831. Mn/Fe_SOD_N.
[Graphical view]
PANTHERiPTHR11404. PTHR11404. 1 hit.
PfamiPF02777. Sod_Fe_C. 1 hit.
PF00081. Sod_Fe_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000349. SODismutase. 1 hit.
PRINTSiPR01703. MNSODISMTASE.
SUPFAMiSSF46609. SSF46609. 1 hit.
SSF54719. SSF54719. 1 hit.
PROSITEiPS00088. SOD_MN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AGD3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSFELPALPY AKDALAPHIS AETIEYHYGK HHQTYVTNLN NLIKGTAFEG
60 70 80 90 100
KSLEEIIRSS EGGVFNNAAQ VWNHTFYWNC LAPNAGGEPT GKVAEAIAAS
110 120 130 140 150
FGSFADFKAQ FTDAAIKNFG SGWTWLVKNS DGKLAIVSTS NAGTPLTTDA
160 170 180 190
TPLLTVDVWE HAYYIDYRNA RPGYLEHFWA LVNWEFVAKN LAA
Length:193
Mass (Da):21,266
Last modified:January 23, 2007 - v2
Checksum:i91236D2A8FE61474
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03511 Genomic DNA. Translation: AAA24637.1.
U00096 Genomic DNA. Translation: AAC74728.1.
AP009048 Genomic DNA. Translation: BAA15422.1.
PIRiA29940. DSECF.
RefSeqiNP_416173.1. NC_000913.3.
YP_489920.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74728; AAC74728; b1656.
BAA15422; BAA15422; BAA15422.
GeneIDi12931271.
944953.
KEGGiecj:Y75_p1633.
eco:b1656.
PATRICi32118616. VBIEscCol129921_1728.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03511 Genomic DNA. Translation: AAA24637.1.
U00096 Genomic DNA. Translation: AAC74728.1.
AP009048 Genomic DNA. Translation: BAA15422.1.
PIRiA29940. DSECF.
RefSeqiNP_416173.1. NC_000913.3.
YP_489920.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ISAX-ray1.80A/B2-193[»]
1ISBX-ray1.85A/B2-193[»]
1ISCX-ray1.80A/B2-193[»]
1ZA5X-ray1.80A/B2-193[»]
2BKBX-ray1.70A/B/C/D2-193[»]
2NYBX-ray1.10A/B/C/D2-193[»]
ProteinModelPortaliP0AGD3.
SMRiP0AGD3. Positions 2-193.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0AGD3. 6 interactions.
STRINGi511145.b1656.

2D gel databases

SWISS-2DPAGEP0AGD3.

Proteomic databases

PaxDbiP0AGD3.
PRIDEiP0AGD3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74728; AAC74728; b1656.
BAA15422; BAA15422; BAA15422.
GeneIDi12931271.
944953.
KEGGiecj:Y75_p1633.
eco:b1656.
PATRICi32118616. VBIEscCol129921_1728.

Organism-specific databases

EchoBASEiEB0947.
EcoGeneiEG10954. sodB.

Phylogenomic databases

eggNOGiCOG0605.
HOGENOMiHOG000013584.
InParanoidiP0AGD3.
KOiK04564.
OMAiGGGNKLP.
OrthoDBiEOG63NMNT.
PhylomeDBiP0AGD3.

Enzyme and pathway databases

BioCyciEcoCyc:SUPEROX-DISMUTFE-MONOMER.
ECOL316407:JW1648-MONOMER.
MetaCyc:SUPEROX-DISMUTFE-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AGD3.
PROiP0AGD3.

Gene expression databases

GenevestigatoriP0AGD3.

Family and domain databases

InterProiIPR001189. Mn/Fe_SOD.
IPR019833. Mn/Fe_SOD_BS.
IPR019832. Mn/Fe_SOD_C.
IPR019831. Mn/Fe_SOD_N.
[Graphical view]
PANTHERiPTHR11404. PTHR11404. 1 hit.
PfamiPF02777. Sod_Fe_C. 1 hit.
PF00081. Sod_Fe_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000349. SODismutase. 1 hit.
PRINTSiPR01703. MNSODISMTASE.
SUPFAMiSSF46609. SSF46609. 1 hit.
SSF54719. SSF54719. 1 hit.
PROSITEiPS00088. SOD_MN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Iron superoxide dismutase. Nucleotide sequence of the gene from Escherichia coli K12 and correlations with crystal structures."
    Carlioz A., Ludwig M.L., Stallings W.C., Fee J.A., Steinman H.M., Touati D.
    J. Biol. Chem. 263:1555-1562(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "The primary structure of iron superoxide dismutase from Escherichia coli."
    Schinina M.E., Maffey L., Barra D., Bossa F., Puget K., Michelson A.M.
    FEBS Lett. 221:87-90(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-193.
  6. "Sequence homologies among bacterial and mitochondrial superoxide dismutases."
    Steinman H.M., Hill R.L.
    Proc. Natl. Acad. Sci. U.S.A. 70:3725-3729(1973) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE.
  7. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-13.
    Strain: K12 / EMG2.
  8. Cited for: PROTEIN SEQUENCE OF 2-5.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  9. "Spectroscopic measurement of a long-predicted active site pK in iron-superoxide dismutase from Escherichia coli."
    Sorkin D.L., Miller A.-F.
    Biochemistry 36:4916-4924(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, COFACTOR.
  10. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  11. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-51, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
  12. "Iron superoxide dismutase from Escherichia coli at 3.1-A resolution: a structure unlike that of copper/zinc protein at both monomer and dimer levels."
    Stallings W.C., Powers T.B., Pattridge K.A., Fee J.A., Ludwig M.L.
    Proc. Natl. Acad. Sci. U.S.A. 80:3884-3888(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH IRON ION, SUBUNIT.

Entry informationi

Entry nameiSODF_ECOLI
AccessioniPrimary (citable) accession number: P0AGD3
Secondary accession number(s): P09157
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 84 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.