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P00445 (SODC_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 172. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Superoxide dismutase [Cu-Zn]

EC=1.15.1.1
Gene names
Name:SOD1
Ordered Locus Names:YJR104C
ORF Names:J1968
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length154 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

2 superoxide + 2 H+ = O2 + H2O2.

Cofactor

Binds 1 copper ion per subunit.

Binds 1 zinc ion per subunit.

Subunit structure

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. Ref.22

Subcellular location

Cytoplasm. Mitochondrion intermembrane space. Note: A small percentage (around 1-5 percent) localizes to the mitochondrial intermembrane space. Ref.9

Miscellaneous

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

Sequence similarities

Belongs to the Cu-Zn superoxide dismutase family.

Ontologies

Keywords
   Cellular componentCytoplasm
Mitochondrion
   LigandCopper
Metal-binding
Zinc
   Molecular functionAntioxidant
Oxidoreductase
   PTMDisulfide bond
Isopeptide bond
Phosphoprotein
Ubl conjugation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processage-dependent response to reactive oxygen species involved in chronological cell aging

Inferred from mutant phenotype PubMed 8647826. Source: SGD

cellular copper ion homeostasis

Inferred from mutant phenotype PubMed 8530401. Source: SGD

cellular zinc ion homeostasis

Inferred from mutant phenotype PubMed 11581253. Source: SGD

fungal-type cell wall organization

Inferred from mutant phenotype PubMed 20176017. Source: SGD

negative regulation of cellular respiration

Inferred from mutant phenotype PubMed 23332757. Source: SGD

positive regulation of sequence-specific DNA binding transcription factor activity

Inferred from mutant phenotype PubMed 18977757. Source: SGD

positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress

Inferred from mutant phenotype PubMed 24647101. Source: SGD

protein stabilization

Inferred from mutant phenotype PubMed 23332757. Source: SGD

removal of superoxide radicals

Inferred from direct assay Ref.1. Source: GOC

superoxide metabolic process

Inferred from mutant phenotype Ref.1. Source: SGD

   Cellular_componentcytosol

Inferred from direct assay Ref.9. Source: SGD

mitochondrial intermembrane space

Inferred from direct assay Ref.9. Source: SGD

nucleus

Inferred from direct assay PubMed 18977757PubMed 24647101. Source: SGD

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction Ref.22PubMed 16429126. Source: IntAct

superoxide dismutase activity

Inferred from direct assay Ref.1. Source: SGD

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CCS1P402022EBI-17635,EBI-10287

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6 Ref.7 Ref.8
Chain2 – 154153Superoxide dismutase [Cu-Zn]
PRO_0000164129

Sites

Metal binding431Zinc 2; shared with CCS1; in apo form
Metal binding471Copper; catalytic
Metal binding491Copper; catalytic
Metal binding641Copper; catalytic
Metal binding641Zinc 1; structural
Metal binding721Zinc 1; structural
Metal binding811Zinc 1; structural
Metal binding841Zinc 1; structural
Metal binding1211Copper; catalytic
Binding site1441Substrate Probable

Amino acid modifications

Modified residue261Phosphoserine Ref.16
Modified residue391Phosphoserine Ref.14 Ref.16 Ref.17
Modified residue991Phosphoserine Ref.15 Ref.16 Ref.17
Modified residue1171Phosphoserine Ref.15
Modified residue1321Phosphothreonine Ref.15
Modified residue1381Phosphothreonine Ref.17
Disulfide bond58 ↔ 147Alternate; alternate Ref.21 Ref.22
Disulfide bond58Interchain (with C-229 in CCS1); alternate Ref.21 Ref.22
Cross-link19Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.11
Cross-link70Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.11

Experimental info

Mutagenesis1231G → K: Does not enable copper chaperone-independent activation. Ref.12
Mutagenesis131 – 1322DT → GN: Does not enable copper chaperone-independent activation.
Mutagenesis1431P → A or S: Enables copper chaperone-independent activation; when associated with A-145 or with L-145. Ref.12 Ref.13
Mutagenesis1451P → A or L: Enables copper chaperone-independent activation; when associated with A-143 or with S-143. Ref.12 Ref.13
Sequence conflict561N → D AA sequence Ref.7
Sequence conflict931N → D AA sequence Ref.7

Secondary structure

.................................. 154
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00445 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: E263A74679AF11F7

FASTA15415,855
        10         20         30         40         50         60 
MVQAVAVLKG DAGVSGVVKF EQASESEPTT VSYEIAGNSP NAERGFHIHE FGDATNGCVS 

        70         80         90        100        110        120 
AGPHFNPFKK THGAPTDEVR HVGDMGNVKT DENGVAKGSF KDSLIKLIGP TSVVGRSVVI 

       130        140        150 
HAGQDDLGKG DTEESLKTGN AGPRPACGVI GLTN 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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]"A structure-based mechanism for copper-zinc superoxide dismutase."
Hart P.J., Balbirnie M.M., Ogihara N.L., Nersissian A.M., Weiss M.S., Valentine J.S., Eisenberg D.
Biochemistry 38:2167-2178(1999) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRDSBYC. A36171.
RefSeqNP_012638.1. NM_001181762.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP00445.
SMRP00445. Positions 2-154.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33860. 209 interactions.
DIPDIP-5859N.
IntActP00445. 4 interactions.
MINTMINT-429649.
STRING4932.YJR104C.

2D gel databases

SWISS-2DPAGEP00445.

Proteomic databases

MaxQBP00445.
PaxDbP00445.
PeptideAtlasP00445.
PRIDEP00445.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYJR104C; YJR104C; YJR104C.
GeneID853568.
KEGGsce:YJR104C.

Organism-specific databases

SGDS000003865. SOD1.

Phylogenomic databases

eggNOGCOG2032.
GeneTreeENSGT00530000063226.
HOGENOMHOG000263447.
KOK04565.
OMATVNARIT.
OrthoDBEOG7HQNMC.

Enzyme and pathway databases

BioCycYEAST:MONOMER3O-1629.

Gene expression databases

GenevestigatorP00445.

Family and domain databases

Gene3D2.60.40.200. 1 hit.
InterProIPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view]
PfamPF00080. Sod_Cu. 1 hit.
[Graphical view]
PRINTSPR00068. CUZNDISMTASE.
SUPFAMSSF49329. SSF49329. 1 hit.
PROSITEPS00087. SOD_CU_ZN_1. 1 hit.
PS00332. SOD_CU_ZN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00445.
NextBio974334.
PROP00445.

Entry information

Entry nameSODC_YEAST
AccessionPrimary (citable) accession number: P00445
Secondary accession number(s): D6VWS3, Q68HB2
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 172 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome X

Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references