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P08294

- SODE_HUMAN

UniProt

P08294 - SODE_HUMAN

Protein

Extracellular superoxide dismutase [Cu-Zn]

Gene

SOD3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 161 (01 Oct 2014)
      Sequence version 2 (30 May 2006)
      Previous versions | rss
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    Functioni

    Protect the extracellular space from toxic effect of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen.

    Catalytic activityi

    2 superoxide + 2 H+ = O2 + H2O2.

    Cofactori

    Binds 1 copper ion per subunit.By similarity
    Binds 1 zinc ion per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei41 – 411Not glycated
    Sitei92 – 921Not glycated
    Metal bindingi114 – 1141Copper; catalytic
    Metal bindingi116 – 1161Copper; catalytic
    Metal bindingi131 – 1311Copper; catalytic
    Metal bindingi131 – 1311Zinc; structural
    Metal bindingi139 – 1391Zinc; structural
    Metal bindingi142 – 1421Zinc; structural
    Metal bindingi145 – 1451Zinc; structural
    Metal bindingi181 – 1811Copper; catalytic
    Sitei238 – 2381Not glycated

    GO - Molecular functioni

    1. copper ion binding Source: RefGenome
    2. heparin binding Source: UniProtKB-KW
    3. protein binding Source: BHF-UCL
    4. superoxide dismutase activity Source: RefGenome
    5. zinc ion binding Source: RefGenome

    GO - Biological processi

    1. removal of superoxide radicals Source: RefGenome
    2. response to copper ion Source: Ensembl
    3. response to hypoxia Source: Ensembl

    Keywords - Molecular functioni

    Antioxidant, Oxidoreductase

    Keywords - Ligandi

    Copper, Heparin-binding, Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiREACT_172715. Detoxification of Reactive Oxygen Species.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Extracellular superoxide dismutase [Cu-Zn] (EC:1.15.1.1)
    Short name:
    EC-SOD
    Gene namesi
    Name:SOD3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 4

    Organism-specific databases

    HGNCiHGNC:11181. SOD3.

    Subcellular locationi

    Secretedextracellular space
    Note: 99% of EC-SOD is anchored to heparan sulfate proteoglycans in the tissue interstitium, and 1% is located in the vasculature in equilibrium between the plasma and the endothelium.

    GO - Cellular componenti

    1. cytoplasm Source: RefGenome
    2. extracellular matrix Source: Ensembl
    3. extracellular region Source: Reactome
    4. extracellular space Source: BHF-UCL
    5. extracellular vesicular exosome Source: UniProt
    6. Golgi lumen Source: Reactome
    7. nucleus Source: Ensembl
    8. trans-Golgi network Source: Ensembl

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA36018.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 1818Add
    BLAST
    Chaini19 – 240222Extracellular superoxide dismutase [Cu-Zn]PRO_0000032855Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi63 ↔ 2081 Publication
    Glycosylationi107 – 1071N-linked (GlcNAc...)2 Publications
    Disulfide bondi125 ↔ 2071 Publication
    Glycosylationi229 – 2291N-linked (Glc) (glycation); in vitro
    Glycosylationi230 – 2301N-linked (Glc) (glycation); in vitro

    Keywords - PTMi

    Disulfide bond, Glycation, Glycoprotein

    Proteomic databases

    MaxQBiP08294.
    PaxDbiP08294.
    PeptideAtlasiP08294.
    PRIDEiP08294.

    PTM databases

    PhosphoSiteiP08294.

    Miscellaneous databases

    PMAP-CutDBP08294.

    Expressioni

    Tissue specificityi

    Expressed in blood vessels, heart, lung, kidney and placenta. Major SOD isoenzyme in extracellular fluids such as plasma, lymph and synovial fluid.

    Gene expression databases

    ArrayExpressiP08294.
    BgeeiP08294.
    CleanExiHS_SOD3.
    GenevestigatoriP08294.

    Organism-specific databases

    HPAiCAB008671.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi9606.ENSP00000371554.

    Structurei

    Secondary structure

    1
    240
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi59 – 679
    Beta strandi79 – 8810
    Beta strandi93 – 1008
    Beta strandi104 – 11714
    Helixi124 – 1285
    Beta strandi145 – 1528
    Beta strandi155 – 16410
    Beta strandi166 – 1694
    Beta strandi176 – 1838
    Beta strandi190 – 1923
    Helixi195 – 1984
    Beta strandi204 – 2096
    Helixi216 – 2227

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2JLPX-ray1.70A/B/C/D19-240[»]
    ProteinModelPortaliP08294.
    SMRiP08294. Positions 55-223.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08294.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the Cu-Zn superoxide dismutase family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG2032.
    HOGENOMiHOG000263447.
    HOVERGENiHBG000062.
    InParanoidiP08294.
    KOiK16627.
    OMAiHPRHPGD.
    PhylomeDBiP08294.
    TreeFamiTF105133.

    Family and domain databases

    Gene3Di2.60.40.200. 1 hit.
    InterProiIPR018152. SOD_Cu/Zn_BS.
    IPR024141. SOD_Cu/Zn_extracel.
    IPR001424. SOD_Cu_Zn_dom.
    [Graphical view]
    PANTHERiPTHR10003:SF36. PTHR10003:SF36. 1 hit.
    PfamiPF00080. Sod_Cu. 1 hit.
    [Graphical view]
    PRINTSiPR00068. CUZNDISMTASE.
    SUPFAMiSSF49329. SSF49329. 1 hit.
    PROSITEiPS00087. SOD_CU_ZN_1. 1 hit.
    PS00332. SOD_CU_ZN_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P08294-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLALLCSCLL LAAGASDAWT GEDSAEPNSD SAEWIRDMYA KVTEIWQEVM    50
    QRRDDDGALH AACQVQPSAT LDAAQPRVTG VVLFRQLAPR AKLDAFFALE 100
    GFPTEPNSSS RAIHVHQFGD LSQGCESTGP HYNPLAVPHP QHPGDFGNFA 150
    VRDGSLWRYR AGLAASLAGP HSIVGRAVVV HAGEDDLGRG GNQASVENGN 200
    AGRRLACCVV GVCGPGLWER QAREHSERKK RRRESECKAA 240
    Length:240
    Mass (Da):25,851
    Last modified:May 30, 2006 - v2
    Checksum:i585B8DEBFC506CF4
    GO

    Polymorphismi

    The variant Gly-231 which is found in about 2.2% of individual displays a 10-fold increased plasma EC-SOD content due to reduced heparin-binding affinity and thus the impairment of its binding ability to endothelial cell surface.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti58 – 581A → T.5 Publications
    Corresponds to variant rs2536512 [ dbSNP | Ensembl ].
    VAR_020776
    Natural varianti91 – 911A → T.1 Publication
    Corresponds to variant rs17879876 [ dbSNP | Ensembl ].
    VAR_020777
    Natural varianti231 – 2311R → G.5 Publications
    Corresponds to variant rs1799895 [ dbSNP | Ensembl ].
    VAR_014705

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02947 mRNA. Translation: AAA66000.1.
    U10116 Genomic DNA. Translation: AAA62278.1.
    CR541853 mRNA. Translation: CAG46651.1.
    AY787834 Genomic DNA. Translation: AAV40827.1.
    BC014418 mRNA. Translation: AAH14418.1.
    CCDSiCCDS3430.1.
    PIRiA28301. DSHUEC.
    RefSeqiNP_003093.2. NM_003102.2.
    UniGeneiHs.2420.

    Genome annotation databases

    EnsembliENST00000382120; ENSP00000371554; ENSG00000109610.
    GeneIDi6649.
    KEGGihsa:6649.
    UCSCiuc003gqz.3. human.

    Polymorphism databases

    DMDMi108885292.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    NIEHS-SNPs
    Wikipedia

    Superoxide dismutase entry

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02947 mRNA. Translation: AAA66000.1 .
    U10116 Genomic DNA. Translation: AAA62278.1 .
    CR541853 mRNA. Translation: CAG46651.1 .
    AY787834 Genomic DNA. Translation: AAV40827.1 .
    BC014418 mRNA. Translation: AAH14418.1 .
    CCDSi CCDS3430.1.
    PIRi A28301. DSHUEC.
    RefSeqi NP_003093.2. NM_003102.2.
    UniGenei Hs.2420.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2JLP X-ray 1.70 A/B/C/D 19-240 [» ]
    ProteinModelPortali P08294.
    SMRi P08294. Positions 55-223.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 9606.ENSP00000371554.

    Chemistry

    ChEMBLi CHEMBL2069159.

    PTM databases

    PhosphoSitei P08294.

    Polymorphism databases

    DMDMi 108885292.

    Proteomic databases

    MaxQBi P08294.
    PaxDbi P08294.
    PeptideAtlasi P08294.
    PRIDEi P08294.

    Protocols and materials databases

    DNASUi 6649.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000382120 ; ENSP00000371554 ; ENSG00000109610 .
    GeneIDi 6649.
    KEGGi hsa:6649.
    UCSCi uc003gqz.3. human.

    Organism-specific databases

    CTDi 6649.
    GeneCardsi GC04P024798.
    HGNCi HGNC:11181. SOD3.
    HPAi CAB008671.
    MIMi 185490. gene.
    neXtProti NX_P08294.
    PharmGKBi PA36018.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2032.
    HOGENOMi HOG000263447.
    HOVERGENi HBG000062.
    InParanoidi P08294.
    KOi K16627.
    OMAi HPRHPGD.
    PhylomeDBi P08294.
    TreeFami TF105133.

    Enzyme and pathway databases

    Reactomei REACT_172715. Detoxification of Reactive Oxygen Species.

    Miscellaneous databases

    ChiTaRSi SOD3. human.
    EvolutionaryTracei P08294.
    GeneWikii SOD3.
    GenomeRNAii 6649.
    NextBioi 25915.
    PMAP-CutDB P08294.
    PROi P08294.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P08294.
    Bgeei P08294.
    CleanExi HS_SOD3.
    Genevestigatori P08294.

    Family and domain databases

    Gene3Di 2.60.40.200. 1 hit.
    InterProi IPR018152. SOD_Cu/Zn_BS.
    IPR024141. SOD_Cu/Zn_extracel.
    IPR001424. SOD_Cu_Zn_dom.
    [Graphical view ]
    PANTHERi PTHR10003:SF36. PTHR10003:SF36. 1 hit.
    Pfami PF00080. Sod_Cu. 1 hit.
    [Graphical view ]
    PRINTSi PR00068. CUZNDISMTASE.
    SUPFAMi SSF49329. SSF49329. 1 hit.
    PROSITEi PS00087. SOD_CU_ZN_1. 1 hit.
    PS00332. SOD_CU_ZN_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation and sequence of complementary DNA encoding human extracellular superoxide dismutase."
      Hjalmarsson K., Marklund S.L., Engstroem A., Edlund T.
      Proc. Natl. Acad. Sci. U.S.A. 84:6340-6344(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, VARIANT THR-58.
    2. "Extracellular superoxide dismutase (SOD3): tissue-specific expression, genomic characterization, and computer-assisted sequence analysis of the human EC SOD gene."
      Folz R.J., Crapo J.D.
      Genomics 22:162-171(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT THR-58.
      Tissue: Blood.
    3. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT THR-58.
    4. NIEHS SNPs program
      Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS THR-58; THR-91 AND GLY-231.
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT THR-58.
      Tissue: Colon.
    6. "The site of nonenzymic glycation of human extracellular-superoxide dismutase in vitro."
      Adachi T., Ohta H., Hayashi K., Hirano K., Marklund S.L.
      Free Radic. Biol. Med. 13:205-210(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCATION AT LYS-229 AND LYS-230.
    7. Cited for: REVIEW.
    8. "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry."
      Liu T., Qian W.-J., Gritsenko M.A., Camp D.G. II, Monroe M.E., Moore R.J., Smith R.D.
      J. Proteome Res. 4:2070-2080(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-107.
      Tissue: Plasma.
    9. "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
      Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
      J. Proteome Res. 8:651-661(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-107.
      Tissue: Liver.
    10. "The structure of human extracellular copper-zinc superoxide dismutase at 1.7 A resolution: insights into heparin and collagen binding."
      Antonyuk S.V., Strange R.W., Marklund S.L., Hasnain S.S.
      J. Mol. Biol. 388:310-326(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 19-240, SUBUNIT, METAL-BINDING SITES, DISULFIDE BONDS.
    11. "10-fold increase in human plasma extracellular superoxide dismutase content caused by a mutation in heparin-binding domain."
      Sandstrom J., Nilsson P., Karlsson K., Marklund S.L.
      J. Biol. Chem. 269:19163-19166(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT GLY-231.
    12. "Molecular analysis of extracellular-superoxide dismutase gene associated with high level in serum."
      Yamada H., Yamada Y., Adachi T., Goto H., Ogasawara N., Futenma A., Kitano M., Hirano K., Kato K.
      Jpn. J. Hum. Genet. 40:177-184(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT GLY-231.
    13. "Substitution of glycine for arginine-213 in extracellular-superoxide dismutase impairs affinity for heparin and endothelial cell surface."
      Adachi T., Yamada H., Yamada Y., Morihara N., Yamazaki N., Murakami T., Futenma A., Kato K., Hirano K.
      Biochem. J. 313:235-239(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT GLY-231.
    14. "An arginine-213 to glycine mutation in human extracellular-superoxide dismutase reduces susceptibility to trypsin-like proteinases."
      Adachi T., Morihara N., Yamazaki N., Yamada H., Futenma A., Kato K., Hirano K.
      J. Biochem. 120:184-188(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT GLY-231.

    Entry informationi

    Entry nameiSODE_HUMAN
    AccessioniPrimary (citable) accession number: P08294
    Secondary accession number(s): Q5U781, Q6FHA2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: May 30, 2006
    Last modified: October 1, 2014
    This is version 161 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

    1. Human chromosome 4
      Human chromosome 4: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3