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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi43 – 431Zinc 2; shared with CCS1; in apo form2 Publications
Metal bindingi47 – 471Copper; catalytic2 Publications
Metal bindingi49 – 491Copper; catalytic2 Publications
Metal bindingi64 – 641Copper; catalytic2 Publications
Metal bindingi64 – 641Zinc 1; structural2 Publications
Metal bindingi72 – 721Zinc 1; structural2 Publications
Metal bindingi81 – 811Zinc 1; structural2 Publications
Metal bindingi84 – 841Zinc 1; structural2 Publications
Metal bindingi121 – 1211Copper; catalytic2 Publications
Binding sitei144 – 1441SubstrateCurated

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)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. 1 Publication
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 methionineiRemoved3 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)
Modified residuei26 – 261PhosphoserineCombined sources
Modified residuei39 – 391PhosphoserineCombined sources
Disulfide bondi58 ↔ 147
Disulfide bondi58 – 58Interchain (with C-229 in CCS1); in linked form
Cross-linki70 – 70Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
Modified residuei99 – 991PhosphoserineCombined sources
Modified residuei117 – 1171PhosphoserineCombined sources
Modified residuei132 – 1321PhosphothreonineCombined sources
Modified residuei138 – 1381PhosphothreonineCombined sources

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 interactions.
DIPiDIP-5859N.
IntActiP00445. 4 interactions.
MINTiMINT-429649.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti56 – 561N → D AA sequence (PubMed:6993479).Curated
Sequence conflicti93 – 931N → D AA sequence (PubMed:6993479).Curated

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
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33860. 214 interactions.
DIPiDIP-5859N.
IntActiP00445. 4 interactions.
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: September 7, 2016
This is version 192 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.