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Protein

Superoxide dismutase [Cu-Zn]

Gene

sod-1

Organism
Caenorhabditis elegans
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 (By similarity). Required for normal brood size (PubMed:18073424). May be involved in regulating mpk-1 phosphorylation downstream of phosphatase ptp-2 during oocyte maturation (PubMed:20380830).By similarity2 Publications

Catalytic activityi

2 superoxide + 2 H+ = O2 + H2O2.

Cofactori

Protein has several cofactor binding sites:
  • Cu cationBy similarityNote: Binds 1 copper ion per subunit.By similarity
  • Zn2+By similarityNote: Binds 1 zinc ion per subunit.By similarity

Enzyme regulationi

The insertion of copper which activates the protein requires glutathione. This is independent of copper chaperone for SOD1 (CCS), which activates orthologs.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi68Copper; catalyticBy similarity1
Metal bindingi70Copper; catalyticBy similarity1
Metal bindingi85Copper; catalyticBy similarity1
Metal bindingi85Zinc; structuralBy similarity1
Metal bindingi93Zinc; structuralBy similarity1
Metal bindingi102Zinc; structuralBy similarity1
Metal bindingi105Zinc; structuralBy similarity1
Metal bindingi142Copper; catalyticBy similarity1

GO - Molecular functioni

  • copper ion binding Source: WormBase
  • protein homodimerization activity Source: UniProtKB
  • superoxide dismutase activity Source: UniProtKB
  • zinc ion binding Source: GO_Central

GO - Biological processi

  • age-dependent response to oxidative stress Source: WormBase
  • oxidation-reduction process Source: WormBase
  • regulation of brood size Source: UniProtKB
  • regulation of vulval development Source: WormBase
  • removal of superoxide radicals Source: WormBase
  • superoxide metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Antioxidant, Oxidoreductase

Keywords - Ligandi

Copper, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Superoxide dismutase [Cu-Zn] (EC:1.15.1.1)
Gene namesi
Name:sod-1
ORF Names:C15F1.7
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome II

Organism-specific databases

WormBaseiC15F1.7a; CE23550; WBGene00004930; sod-1.
C15F1.7b; CE20508; WBGene00004930; sod-1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: WormBase
  • mitochondrion Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Worms exhibit increased oxidative stress and reduced brood size (PubMed:18073424). RNAi-mediated knockdown suppresses the slow germline development and the delayed egg-production of clk-1 mutants (PubMed:14657502). RNAi-mediated knockdown causes an increase in the number of oocytes with mpk-1 phosphorylation (PubMed:20380830).3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi167A → P: Abolishes enzyme activation but has no affect on disulfide bond formation or dimer formation; when associated with A-169. 1 Publication1
Mutagenesisi169A → P: Abolishes enzyme activation but has no affect on disulfide bond formation or dimer formation; when associated with A-167. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Sequence analysisAdd BLAST19
ChainiPRO_000016410220 – 180Superoxide dismutase [Cu-Zn]Add BLAST161

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi79 ↔ 171By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

EPDiP34697.
PaxDbiP34697.
PeptideAtlasiP34697.
PRIDEiP34697.

Expressioni

Gene expression databases

BgeeiWBGene00004930.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi39479. 1 interactor.
IntActiP34697. 1 interactor.
STRINGi6239.C15F1.7a.

Structurei

Secondary structure

1180
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi26 – 32Combined sources7
Beta strandi37 – 43Combined sources7
Beta strandi52 – 59Combined sources8
Beta strandi65 – 71Combined sources7
Turni76 – 79Combined sources4
Helixi80 – 82Combined sources3
Beta strandi93 – 95Combined sources3
Helixi96 – 99Combined sources4
Beta strandi105 – 109Combined sources5
Beta strandi115 – 121Combined sources7
Beta strandi127 – 130Combined sources4
Beta strandi137 – 142Combined sources6
Helixi153 – 155Combined sources3
Helixi156 – 162Combined sources7
Turni164 – 167Combined sources4
Beta strandi168 – 176Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3KBEX-ray1.10A24-180[»]
3KBFX-ray1.30A24-180[»]
ProteinModelPortaliP34697.
SMRiP34697.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP34697.

Family & Domainsi

Sequence similaritiesi

Belongs to the Cu-Zn superoxide dismutase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG0441. Eukaryota.
COG2032. LUCA.
GeneTreeiENSGT00530000063226.
HOGENOMiHOG000263447.
InParanoidiP34697.
KOiK04565.
OMAiTIFFTHE.
OrthoDBiEOG091G0OG2.
PhylomeDBiP34697.

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]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform a (identifier: P34697-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFMNLLTQVS NAIFPQVEAA QKMSNRAVAV LRGETVTGTI WITQKSENDQ
60 70 80 90 100
AVIEGEIKGL TPGLHGFHVH QYGDSTNGCI SAGPHFNPFG KTHGGPKSEI
110 120 130 140 150
RHVGDLGNVE AGADGVAKIK LTDTLVTLYG PNTVVGRSMV VHAGQDDLGE
160 170 180
GVGDKAEESK KTGNAGARAA CGVIALAAPQ
Note: No experimental confirmation available.
Length:180
Mass (Da):18,700
Last modified:April 29, 2008 - v2
Checksum:i5F013D99A650AA97
GO
Isoform b (identifier: P34697-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-22: Missing.

Show »
Length:158
Mass (Da):16,237
Checksum:i0B4A19EAFF87CF33
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0331461 – 22Missing in isoform b. 1 PublicationAdd BLAST22

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L20135 mRNA. Translation: AAA28147.1.
X77020 Genomic DNA. Translation: CAA54318.1.
FO080553 Genomic DNA. Translation: CCD64617.1.
FO080553 Genomic DNA. Translation: CCD64618.1.
PIRiS41319. A48256.
RefSeqiNP_001021956.1. NM_001026785.2. [P34697-1]
NP_001021957.1. NM_001026786.3. [P34697-2]
UniGeneiCel.19756.

Genome annotation databases

EnsemblMetazoaiC15F1.7a; C15F1.7a; WBGene00004930. [P34697-1]
GeneIDi174141.
KEGGicel:CELE_C15F1.7.
UCSCiC15F1.7a. c. elegans. [P34697-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L20135 mRNA. Translation: AAA28147.1.
X77020 Genomic DNA. Translation: CAA54318.1.
FO080553 Genomic DNA. Translation: CCD64617.1.
FO080553 Genomic DNA. Translation: CCD64618.1.
PIRiS41319. A48256.
RefSeqiNP_001021956.1. NM_001026785.2. [P34697-1]
NP_001021957.1. NM_001026786.3. [P34697-2]
UniGeneiCel.19756.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3KBEX-ray1.10A24-180[»]
3KBFX-ray1.30A24-180[»]
ProteinModelPortaliP34697.
SMRiP34697.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi39479. 1 interactor.
IntActiP34697. 1 interactor.
STRINGi6239.C15F1.7a.

Proteomic databases

EPDiP34697.
PaxDbiP34697.
PeptideAtlasiP34697.
PRIDEiP34697.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC15F1.7a; C15F1.7a; WBGene00004930. [P34697-1]
GeneIDi174141.
KEGGicel:CELE_C15F1.7.
UCSCiC15F1.7a. c. elegans. [P34697-1]

Organism-specific databases

CTDi174141.
WormBaseiC15F1.7a; CE23550; WBGene00004930; sod-1.
C15F1.7b; CE20508; WBGene00004930; sod-1.

Phylogenomic databases

eggNOGiKOG0441. Eukaryota.
COG2032. LUCA.
GeneTreeiENSGT00530000063226.
HOGENOMiHOG000263447.
InParanoidiP34697.
KOiK04565.
OMAiTIFFTHE.
OrthoDBiEOG091G0OG2.
PhylomeDBiP34697.

Miscellaneous databases

EvolutionaryTraceiP34697.
PROiP34697.

Gene expression databases

BgeeiWBGene00004930.

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_CAEEL
AccessioniPrimary (citable) accession number: P34697
Secondary accession number(s): Q5W7E8, Q9N5Y1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: April 29, 2008
Last modified: November 2, 2016
This is version 139 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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.