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Protein

Superoxide dismutase [Cu-Zn]

Gene

SOD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:
  • Cu cationNote: Binds 1 copper ion per subunit.
  • Zn2+Note: Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi43Zinc 2; shared with CCS1; in apo form2 Publications1
Metal bindingi47Copper; catalytic2 Publications1
Metal bindingi49Copper; catalytic2 Publications1
Metal bindingi64Copper; catalytic2 Publications1
Metal bindingi64Zinc 1; structural2 Publications1
Metal bindingi72Zinc 1; structural2 Publications1
Metal bindingi81Zinc 1; structural2 Publications1
Metal bindingi84Zinc 1; structural2 Publications1
Metal bindingi121Copper; catalytic2 Publications1
Binding sitei144SubstrateCurated1

GO - Molecular functioni

  • copper ion binding Source: GO_Central
  • superoxide dismutase activity Source: SGD
  • zinc ion binding Source: GO_Central

GO - Biological processi

  • age-dependent response to reactive oxygen species involved in chronological cell aging Source: SGD
  • cellular copper ion homeostasis Source: SGD
  • cellular zinc ion homeostasis Source: SGD
  • fungal-type cell wall organization Source: SGD
  • negative regulation of cellular respiration Source: SGD
  • positive regulation of sequence-specific DNA binding transcription factor activity Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress Source: SGD
  • protein stabilization Source: SGD
  • 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.
ReactomeiR-SCE-114608. Platelet degranulation.
R-SCE-3299685. 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
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJR104C.
SGDiS000003865. SOD1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrial intermembrane space Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi123G → K: Does not enable copper chaperone-independent activation. 1 Publication1
Mutagenesisi131 – 132DT → GN: Does not enable copper chaperone-independent activation. 1 Publication2
Mutagenesisi143P → A or S: Enables copper chaperone-independent activation; when associated with A-145 or with L-145. 2 Publications1
Mutagenesisi145P → A or L: Enables copper chaperone-independent activation; when associated with A-143 or with S-143. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved3 Publications
ChainiPRO_00001641292 – 154Superoxide dismutase [Cu-Zn]Add BLAST153

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki19Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication
Modified residuei26PhosphoserineCombined sources1
Modified residuei39PhosphoserineCombined sources1
Disulfide bondi58 ↔ 147
Disulfide bondi58Interchain (with C-229 in CCS1); in linked form
Cross-linki70Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication
Modified residuei99PhosphoserineCombined sources1
Modified residuei117PhosphoserineCombined sources1
Modified residuei132PhosphothreonineCombined sources1
Modified residuei138PhosphothreonineCombined sources1

Keywords - PTMi

Disulfide bond, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP00445.
PRIDEiP00445.
TopDownProteomicsiP00445.

2D gel databases

SWISS-2DPAGEP00445.

PTM databases

iPTMnetiP00445.

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.3 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi33860. 214 interactors.
DIPiDIP-5859N.
IntActiP00445. 4 interactors.
MINTiMINT-429649.

Structurei

Secondary structure

1154
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 9Combined sources7
Beta strandi11 – 13Combined sources3
Beta strandi15 – 21Combined sources7
Beta strandi23 – 27Combined sources5
Beta strandi29 – 37Combined sources9
Beta strandi43 – 50Combined sources8
Turni55 – 58Combined sources4
Helixi59 – 61Combined sources3
Beta strandi77 – 80Combined sources4
Beta strandi84 – 89Combined sources6
Beta strandi96 – 104Combined sources9
Beta strandi107 – 109Combined sources3
Beta strandi116 – 120Combined sources5
Beta strandi130 – 132Combined sources3
Helixi135 – 138Combined sources4
Beta strandi146 – 149Combined sources4
Beta strandi151 – 153Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00445.

Family & Domainsi

Sequence similaritiesi

Belongs to the Cu-Zn superoxide dismutase family.Curated

Phylogenomic databases

GeneTreeiENSGT00530000063226.
HOGENOMiHOG000263447.
InParanoidiP00445.
KOiK04565.
OMAiVCVLKGT.
OrthoDBiEOG092C578I.

Family and domain databases

CDDicd00305. Cu-Zn_Superoxide_Dismutase. 1 hit.
Gene3Di2.60.40.200. 1 hit.
InterProiIPR024134. SOD_Cu/Zn_/chaperone.
IPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view]
PANTHERiPTHR10003. PTHR10003. 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.

P00445-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVQAVAVLKG DAGVSGVVKF EQASESEPTT VSYEIAGNSP NAERGFHIHE
60 70 80 90 100
FGDATNGCVS AGPHFNPFKK THGAPTDEVR HVGDMGNVKT DENGVAKGSF
110 120 130 140 150
KDSLIKLIGP TSVVGRSVVI HAGQDDLGKG DTEESLKTGN AGPRPACGVI

GLTN
Length:154
Mass (Da):15,855
Last modified:January 23, 2007 - v2
Checksum:iE263A74679AF11F7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti56N → D AA sequence (PubMed:6993479).Curated1
Sequence conflicti93N → D AA sequence (PubMed:6993479).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33860. 214 interactors.
DIPiDIP-5859N.
IntActiP00445. 4 interactors.
MINTiMINT-429649.

PTM databases

iPTMnetiP00445.

2D gel databases

SWISS-2DPAGEP00445.

Proteomic databases

MaxQBiP00445.
PRIDEiP00445.
TopDownProteomicsiP00445.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YJR104C.
SGDiS000003865. SOD1.

Phylogenomic databases

GeneTreeiENSGT00530000063226.
HOGENOMiHOG000263447.
InParanoidiP00445.
KOiK04565.
OMAiVCVLKGT.
OrthoDBiEOG092C578I.

Enzyme and pathway databases

BioCyciYEAST:MONOMER3O-1629.
ReactomeiR-SCE-114608. Platelet degranulation.
R-SCE-3299685. Detoxification of Reactive Oxygen Species.

Miscellaneous databases

EvolutionaryTraceiP00445.
PROiP00445.

Family and domain databases

CDDicd00305. Cu-Zn_Superoxide_Dismutase. 1 hit.
Gene3Di2.60.40.200. 1 hit.
InterProiIPR024134. SOD_Cu/Zn_/chaperone.
IPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view]
PANTHERiPTHR10003. PTHR10003. 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]
ProtoNetiSearch...

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: November 2, 2016
This is version 193 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.1 Publication

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

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 one 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.