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P0AGD3

- SODF_ECOLI

UniProt

P0AGD3 - SODF_ECOLI

Protein

Superoxide dismutase [Fe]

Gene

sodB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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

    Binds 1 iron ion 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: EcoCyc

    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

    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

    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 – 187
    Helixi21 – 299
    Helixi31 – 4313
    Turni47 – 504
    Helixi53 – 575
    Helixi62 – 7918
    Helixi91 – 10111
    Helixi104 – 11714
    Beta strandi120 – 1289
    Beta strandi134 – 1407
    Helixi145 – 1473
    Beta strandi151 – 1577
    Helixi160 – 1623
    Helixi164 – 1674
    Helixi171 – 1799
    Helixi184 – 1929

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK04564.
    OMAiWTWLVKG.
    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

    MSFELPALPY AKDALAPHIS AETIEYHYGK HHQTYVTNLN NLIKGTAFEG    50
    KSLEEIIRSS EGGVFNNAAQ VWNHTFYWNC LAPNAGGEPT GKVAEAIAAS 100
    FGSFADFKAQ FTDAAIKNFG SGWTWLVKNS DGKLAIVSTS NAGTPLTTDA 150
    TPLLTVDVWE HAYYIDYRNA RPGYLEHFWA LVNWEFVAKN LAA 193
    Length:193
    Mass (Da):21,266
    Last modified:January 23, 2007 - v2
    Checksum:i91236D2A8FE61474
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03511 Genomic DNA. Translation: AAA24637.1 .
    U00096 Genomic DNA. Translation: AAC74728.1 .
    AP009048 Genomic DNA. Translation: BAA15422.1 .
    PIRi A29940. DSECF.
    RefSeqi NP_416173.1. NC_000913.3.
    YP_489920.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ISA X-ray 1.80 A/B 2-193 [» ]
    1ISB X-ray 1.85 A/B 2-193 [» ]
    1ISC X-ray 1.80 A/B 2-193 [» ]
    1ZA5 X-ray 1.80 A/B 2-193 [» ]
    2BKB X-ray 1.70 A/B/C/D 2-193 [» ]
    2NYB X-ray 1.10 A/B/C/D 2-193 [» ]
    ProteinModelPortali P0AGD3.
    SMRi P0AGD3. Positions 2-193.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P0AGD3. 6 interactions.
    STRINGi 511145.b1656.

    2D gel databases

    SWISS-2DPAGE P0AGD3.

    Proteomic databases

    PaxDbi P0AGD3.
    PRIDEi P0AGD3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74728 ; AAC74728 ; b1656 .
    BAA15422 ; BAA15422 ; BAA15422 .
    GeneIDi 12931271.
    944953.
    KEGGi ecj:Y75_p1633.
    eco:b1656.
    PATRICi 32118616. VBIEscCol129921_1728.

    Organism-specific databases

    EchoBASEi EB0947.
    EcoGenei EG10954. sodB.

    Phylogenomic databases

    eggNOGi COG0605.
    HOGENOMi HOG000013584.
    KOi K04564.
    OMAi WTWLVKG.
    OrthoDBi EOG63NMNT.
    PhylomeDBi P0AGD3.

    Enzyme and pathway databases

    BioCyci EcoCyc:SUPEROX-DISMUTFE-MONOMER.
    ECOL316407:JW1648-MONOMER.
    MetaCyc:SUPEROX-DISMUTFE-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AGD3.
    PROi P0AGD3.

    Gene expression databases

    Genevestigatori P0AGD3.

    Family and domain databases

    InterProi IPR001189. Mn/Fe_SOD.
    IPR019833. Mn/Fe_SOD_BS.
    IPR019832. Mn/Fe_SOD_C.
    IPR019831. Mn/Fe_SOD_N.
    [Graphical view ]
    PANTHERi PTHR11404. PTHR11404. 1 hit.
    Pfami PF02777. Sod_Fe_C. 1 hit.
    PF00081. Sod_Fe_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000349. SODismutase. 1 hit.
    PRINTSi PR01703. MNSODISMTASE.
    SUPFAMi SSF46609. SSF46609. 1 hit.
    SSF54719. SSF54719. 1 hit.
    PROSITEi PS00088. SOD_MN. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 81 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