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P00445

- SODC_YEAST

UniProt

P00445 - SODC_YEAST

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Protein

Superoxide dismutase [Cu-Zn]

Gene
SOD1, YJR104C, J1968
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

2 superoxide + 2 H+ = O2 + H2O2.

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi43 – 431Zinc 2; shared with CCS1; in apo form
Metal bindingi47 – 471Copper; catalytic
Metal bindingi49 – 491Copper; catalytic
Metal bindingi64 – 641Copper; catalytic
Metal bindingi64 – 641Zinc 1; structural
Metal bindingi72 – 721Zinc 1; structural
Metal bindingi81 – 811Zinc 1; structural
Metal bindingi84 – 841Zinc 1; structural
Metal bindingi121 – 1211Copper; catalytic
Binding sitei144 – 1441Substrate Inferred

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. protein binding Source: IntAct
  3. superoxide dismutase activity Source: SGD

GO - Biological processi

  1. age-dependent response to reactive oxygen species involved in chronological cell aging Source: SGD
  2. cellular copper ion homeostasis Source: SGD
  3. cellular zinc ion homeostasis Source: SGD
  4. fungal-type cell wall organization Source: SGD
  5. negative regulation of cellular respiration Source: SGD
  6. positive regulation of sequence-specific DNA binding transcription factor activity Source: SGD
  7. positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress Source: SGD
  8. protein stabilization Source: SGD
  9. removal of superoxide radicals Source: GOC
  10. superoxide metabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Antioxidant, Oxidoreductase

Keywords - Ligandi

Copper, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:MONOMER3O-1629.
ReactomeiREACT_191152. Detoxification of Reactive Oxygen Species.

Names & Taxonomyi

Protein namesi
Recommended name:
Superoxide dismutase [Cu-Zn] (EC:1.15.1.1)
Gene namesi
Name:SOD1
Ordered Locus Names:YJR104C
ORF Names:J1968
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome X

Organism-specific databases

SGDiS000003865. SOD1.

Subcellular locationi

Cytoplasm. Mitochondrion intermembrane space
Note: A small percentage (around 1-5 percent) localizes to the mitochondrial intermembrane space.1 Publication

GO - Cellular componenti

  1. cytosol Source: SGD
  2. mitochondrial intermembrane space Source: SGD
  3. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi123 – 1231G → K: Does not enable copper chaperone-independent activation. 1 Publication
Mutagenesisi131 – 1322DT → GN: Does not enable copper chaperone-independent activation.
Mutagenesisi143 – 1431P → A or S: Enables copper chaperone-independent activation; when associated with A-145 or with L-145. 2 Publications
Mutagenesisi145 – 1451P → A or L: Enables copper chaperone-independent activation; when associated with A-143 or with S-143. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed3 Publications
Chaini2 – 154153Superoxide dismutase [Cu-Zn]PRO_0000164129Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki19 – 19Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication
Modified residuei26 – 261Phosphoserine1 Publication
Modified residuei39 – 391Phosphoserine3 Publications
Disulfide bondi58 ↔ 147
Disulfide bondi58 – 58Interchain (with C-229 in CCS1); in linked form2 Publications
Cross-linki70 – 70Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication
Modified residuei99 – 991Phosphoserine3 Publications
Modified residuei117 – 1171Phosphoserine1 Publication
Modified residuei132 – 1321Phosphothreonine1 Publication
Modified residuei138 – 1381Phosphothreonine1 Publication

Keywords - PTMi

Disulfide bond, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP00445.
PaxDbiP00445.
PeptideAtlasiP00445.
PRIDEiP00445.

2D gel databases

SWISS-2DPAGEP00445.

Expressioni

Gene expression databases

GenevestigatoriP00445.

Interactioni

Subunit structurei

Homodimer in holo form. In apo form, heterodimer with CCS1. Zinc-binding at 'His-16' of CCS1 and Glu-43 of apo-SOD1 is required for this heterodimerization.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
CCS1P402022EBI-17635,EBI-10287

Protein-protein interaction databases

BioGridi33860. 209 interactions.
DIPiDIP-5859N.
IntActiP00445. 4 interactions.
MINTiMINT-429649.
STRINGi4932.YJR104C.

Structurei

Secondary structure

1
154
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97
Beta strandi11 – 133
Beta strandi15 – 217
Beta strandi23 – 275
Beta strandi29 – 379
Beta strandi43 – 508
Turni55 – 584
Helixi59 – 613
Beta strandi77 – 804
Beta strandi84 – 896
Beta strandi96 – 1049
Beta strandi107 – 1093
Beta strandi116 – 1205
Beta strandi130 – 1323
Helixi135 – 1384
Beta strandi146 – 1494
Beta strandi151 – 1533

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B4LX-ray1.80A2-154[»]
1B4TX-ray1.80A2-154[»]
1F18X-ray1.70A1-154[»]
1F1AX-ray1.80A1-154[»]
1F1DX-ray2.10A1-154[»]
1F1GX-ray1.35A/B/C/D/E/F1-154[»]
1JCVX-ray1.55A2-154[»]
1JK9X-ray2.90A/C2-154[»]
1SDYX-ray2.50A/B/C/D2-154[»]
1YAZX-ray1.70A2-154[»]
1YSOX-ray1.73A2-154[»]
2JCWX-ray1.70A2-154[»]
ProteinModelPortaliP00445.
SMRiP00445. Positions 2-154.

Miscellaneous databases

EvolutionaryTraceiP00445.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG2032.
GeneTreeiENSGT00530000063226.
HOGENOMiHOG000263447.
KOiK04565.
OMAiTVNARIT.
OrthoDBiEOG7HQNMC.

Family and domain databases

Gene3Di2.60.40.200. 1 hit.
InterProiIPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view]
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.

P00445-1 [UniParc]FASTAAdd to Basket

« Hide

MVQAVAVLKG DAGVSGVVKF EQASESEPTT VSYEIAGNSP NAERGFHIHE    50
FGDATNGCVS AGPHFNPFKK THGAPTDEVR HVGDMGNVKT DENGVAKGSF 100
KDSLIKLIGP TSVVGRSVVI HAGQDDLGKG DTEESLKTGN AGPRPACGVI 150
GLTN 154
Length:154
Mass (Da):15,855
Last modified:January 23, 2007 - v2
Checksum:iE263A74679AF11F7
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti56 – 561N → D AA sequence 1 Publication
Sequence conflicti93 – 931N → D AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J03279 Genomic DNA. Translation: AAA34543.1.
AY690619 Genomic DNA. Translation: AAT99430.1.
Z49604 Genomic DNA. Translation: CAA89634.1.
AY558073 Genomic DNA. Translation: AAS56399.1.
BK006943 Genomic DNA. Translation: DAA08889.1.
PIRiA36171. DSBYC.
RefSeqiNP_012638.1. NM_001181762.1.

Genome annotation databases

EnsemblFungiiYJR104C; YJR104C; YJR104C.
GeneIDi853568.
KEGGisce:YJR104C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J03279 Genomic DNA. Translation: AAA34543.1 .
AY690619 Genomic DNA. Translation: AAT99430.1 .
Z49604 Genomic DNA. Translation: CAA89634.1 .
AY558073 Genomic DNA. Translation: AAS56399.1 .
BK006943 Genomic DNA. Translation: DAA08889.1 .
PIRi A36171. DSBYC.
RefSeqi NP_012638.1. NM_001181762.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1B4L X-ray 1.80 A 2-154 [» ]
1B4T X-ray 1.80 A 2-154 [» ]
1F18 X-ray 1.70 A 1-154 [» ]
1F1A X-ray 1.80 A 1-154 [» ]
1F1D X-ray 2.10 A 1-154 [» ]
1F1G X-ray 1.35 A/B/C/D/E/F 1-154 [» ]
1JCV X-ray 1.55 A 2-154 [» ]
1JK9 X-ray 2.90 A/C 2-154 [» ]
1SDY X-ray 2.50 A/B/C/D 2-154 [» ]
1YAZ X-ray 1.70 A 2-154 [» ]
1YSO X-ray 1.73 A 2-154 [» ]
2JCW X-ray 1.70 A 2-154 [» ]
ProteinModelPortali P00445.
SMRi P00445. Positions 2-154.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33860. 209 interactions.
DIPi DIP-5859N.
IntActi P00445. 4 interactions.
MINTi MINT-429649.
STRINGi 4932.YJR104C.

2D gel databases

SWISS-2DPAGE P00445.

Proteomic databases

MaxQBi P00445.
PaxDbi P00445.
PeptideAtlasi P00445.
PRIDEi P00445.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YJR104C ; YJR104C ; YJR104C .
GeneIDi 853568.
KEGGi sce:YJR104C.

Organism-specific databases

SGDi S000003865. SOD1.

Phylogenomic databases

eggNOGi COG2032.
GeneTreei ENSGT00530000063226.
HOGENOMi HOG000263447.
KOi K04565.
OMAi TVNARIT.
OrthoDBi EOG7HQNMC.

Enzyme and pathway databases

BioCyci YEAST:MONOMER3O-1629.
Reactomei REACT_191152. Detoxification of Reactive Oxygen Species.

Miscellaneous databases

EvolutionaryTracei P00445.
NextBioi 974334.
PROi P00445.

Gene expression databases

Genevestigatori P00445.

Family and domain databases

Gene3Di 2.60.40.200. 1 hit.
InterProi IPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view ]
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

« Hide 'large scale' publications
  1. "The copper, zinc-superoxide dismutase gene of Saccharomyces cerevisiae: cloning, sequencing, and biological activity."
    Bermingham-Mcdonogh O., Gralla E., Valentine J.
    Proc. Natl. Acad. Sci. U.S.A. 85:4789-4793(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Cloning and sequence analysis of copper, zinc-superoxide dismutase gene."
    Ping Y.
    Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. "The complete amino acid sequence of copper, zinc superoxide dismutase from Saccharomyces cerevisiae."
    Johansen J.T., Overballe-Petersen C., Martin B., Hasemann V., Svendsen I.
    Carlsberg Res. Commun. 44:201-217(1979)
    Cited for: PROTEIN SEQUENCE OF 2-154.
  7. "The amino acid sequence of copper-zinc superoxide dismutase from bakers' yeast."
    Steinman H.M.
    J. Biol. Chem. 255:6758-6765(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-154.
  8. Frutiger S., Hughes G.J., Sanchez J.-C., Hochstrasser D.F.
    Submitted (FEB-1996) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-11.
    Strain: ATCC 26786 / X2180-1A.
  9. "A fraction of yeast Cu,Zn-superoxide dismutase and its metallochaperone, CCS, localize to the intermembrane space of mitochondria. A physiological role for SOD1 in guarding against mitochondrial oxidative damage."
    Sturtz L.A., Diekert K., Jensen L.T., Lill R., Culotta V.C.
    J. Biol. Chem. 276:38084-38089(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses."
    Zhou W., Ryan J.J., Zhou H.
    J. Biol. Chem. 279:32262-32268(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-19 AND LYS-70.
  12. "Mechanisms for activating Cu- and Zn-containing superoxide dismutase in the absence of the CCS Cu chaperone."
    Carroll M.C., Girouard J.B., Ulloa J.L., Subramaniam J.R., Wong P.C., Valentine J.S., Culotta V.C.
    Proc. Natl. Acad. Sci. U.S.A. 101:5964-5969(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLY-123; 131-ASP-THR-132; PRO-143 AND PRO-145.
  13. "Activation of CuZn superoxide dismutases from Caenorhabditis elegans does not require the copper chaperone CCS."
    Jensen L.T., Culotta V.C.
    J. Biol. Chem. 280:41373-41379(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF PRO-143 AND PRO-145.
  14. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
    Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
    Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-39, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: YAL6B.
  15. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99; SER-117 AND THR-132, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26; SER-39 AND SER-99, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-39; SER-99 AND THR-138, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. "Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase."
    Djinovic K., Gatti G., Coda A., Antolini L., Pelosi G., Desideri A., Falconi M., Marmocchi F., Rotilio G., Bolognesi M.
    Acta Crystallogr. B 47:918-927(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  19. "Crystal structure of yeast Cu,Zn superoxide dismutase. Crystallographic refinement at 2.5-A resolution."
    Djinovic K., Gatti G., Coda A., Antolini L., Pelosi G., Desideri A., Falconi M., Marmocchi F., Rotilio G., Bolognesi M.
    J. Mol. Biol. 225:791-809(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  20. "Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase."
    Ogihara N.L., Parge H.E., Hart P.J., Weiss M.S., Goto J.J., Crane B.R., Tsang J., Slater K., Roe J.A., Valentine J.S., Eisenberg D., Tainer J.A.
    Biochemistry 35:2316-2321(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH COPPER AND ZINC IONS.
  21. Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG; COPPER AND ZINC, DISULFIDE BONDS.
  22. "Heterodimeric structure of superoxide dismutase in complex with its metallochaperone."
    Lamb A.L., Torres A.S., O'Halloran T.V., Rosenzweig A.C.
    Nat. Struct. Biol. 8:751-755(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH ZINC AND CCS1, SUBUNIT, DISULFIDE BONDS.

Entry informationi

Entry nameiSODC_YEAST
AccessioniPrimary (citable) accession number: P00445
Secondary accession number(s): D6VWS3, Q68HB2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: September 3, 2014
This is version 173 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 519000 molecules/cell in log phase SD medium.

Keywords - Technical termi

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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

External Data

Dasty 3

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