P00445 (SODC_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Superoxide dismutase [Cu-Zn]
EC=1.15.1.1

Gene names

Name:	SOD1
Ordered Locus Names:	YJR104C
ORF Names:	J1968

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	154 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 component	Cytoplasm Mitochondrion
Ligand	Copper Metal-binding Zinc
Molecular function	Antioxidant Oxidoreductase
PTM	Disulfide bond Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	age-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 genetic interaction 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 positive regulation of sequence-specific DNA binding transcription factor activity Inferred from mutant phenotype PubMed 18977757. Source: SGD removal of superoxide radicals Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	cytosol 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 18977757. Source: SGD
Molecular_function	copper ion binding Inferred from Biological aspect of Ancestor. Source: RefGenome superoxide dismutase activity Inferred from direct assay Ref.1. Source: SGD zinc ion binding Inferred from Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CCS1	P40202	2	EBI-17635,EBI-10287

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6 Ref.7 Ref.8

Chain

2 – 154

153

Superoxide dismutase [Cu-Zn]

PRO_0000164129

Sites

Metal binding

43

1

Zinc 2; shared with CCS1; in apo form

Metal binding

47

1

Copper; catalytic

Metal binding

49

1

Copper; catalytic

Metal binding

64

1

Copper; catalytic

Metal binding

64

1

Zinc 1; structural

Metal binding

72

1

Zinc 1; structural

Metal binding

81

1

Zinc 1; structural

Metal binding

84

1

Zinc 1; structural

Metal binding

121

1

Copper; catalytic

Binding site

144

1

Substrate Probable

Amino acid modifications

Modified residue

15

1

Phosphoserine Ref.17

Modified residue

24

1

Phosphoserine Ref.17

Modified residue

26

1

Phosphoserine Ref.17

Modified residue

39

1

Phosphoserine Ref.14 Ref.16 Ref.17

Modified residue

99

1

Phosphoserine Ref.15 Ref.16 Ref.17

Modified residue

103

1

Phosphoserine Ref.17

Modified residue

112

1

Phosphoserine Ref.15

Modified residue

117

1

Phosphoserine Ref.15

Modified residue

132

1

Phosphothreonine Ref.15

Disulfide bond

58 ↔ 147

Alternate Ref.21 Ref.22

Disulfide bond

58

Interchain (with C-229 in CCS1); alternate Ref.21 Ref.22

Cross-link

19

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.11

Cross-link

70

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.11

Experimental info

Mutagenesis

123

1

G → K: Does not enable copper chaperone-independent activation. Ref.12

Mutagenesis

131 – 132

2

DT → GN: Does not enable copper chaperone-independent activation.

Mutagenesis

143

1

P → A or S: Enables copper chaperone-independent activation; when associated with A-145 or with L-145. Ref.12 Ref.13

Mutagenesis

145

1

P → A or L: Enables copper chaperone-independent activation; when associated with A-143 or with S-143. Ref.12 Ref.13

Sequence conflict

56

1

N → D AA sequence Ref.7

Sequence conflict

93

1

N → D AA sequence Ref.7

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

154

Helix Strand Turn

Details...

Beta strand

3 – 9

7

Beta strand

11 – 13

3

Beta strand

15 – 21

7

Beta strand

23 – 27

5

Beta strand

29 – 37

9

Beta strand

43 – 50

8

Turn

55 – 58

4

Helix

59 – 61

3

Beta strand

77 – 80

4

Beta strand

84 – 89

6

Beta strand

96 – 104

9

Beta strand

107 – 109

3

Beta strand

116 – 120

5

Beta strand

130 – 132

3

Helix

135 – 138

4

Beta strand

146 – 149

4

Beta strand

151 – 153

3

Sequences

	Sequence		Length	Mass (Da)
	P00445 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: E263A74679AF11F7	FASTA	154	15,855
	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

References

	« Hide 'large scale' referencesShow '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. , 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 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. , 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, MASS SPECTROMETRY.
[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, MASS SPECTROMETRY. 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-112; SER-117 AND THR-132, MASS SPECTROMETRY.
[16]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-39 AND SER-99, MASS SPECTROMETRY.
[17]	"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-15; SER-24; SER-26; SER-39; SER-99 AND SER-103, MASS SPECTROMETRY.
[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.

PIR

DSBYC. A36171.

RefSeq

NP_012638.1. NM_001181762.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P00445.

SMR

P00445. Positions 2-154.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5859N.

IntAct

P00445. 10 interactions.

MINT

MINT-429649.

STRING

4932.YJR104C.

2D gel databases

SWISS-2DPAGE

P00445.

Proteomic databases

PaxDb

P00445.

PeptideAtlas

P00445.

PRIDE

P00445.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YJR104C; YJR104C; YJR104C.

GeneID

853568.

KEGG

sce:YJR104C.

Organism-specific databases

SGD

S000003865. SOD1.

Phylogenomic databases

eggNOG

COG2032.

GeneTree

ENSGT00530000063226.

HOGENOM

HOG000263447.

KO

K04565.

OMA

FEAITIS.

OrthoDB

EOG4X3M9S.

Enzyme and pathway databases

BioCyc

YEAST:MONOMER3O-1629.

Gene expression databases

Genevestigator

P00445.

GermOnline

YJR104C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.60.40.200. 1 hit.

InterPro

IPR024134. SOD_Cu/Zn_/chaperones.
IPR018152. SOD_Cu/Zn_BS.
IPR001424. SOD_Cu_Zn_dom.
[Graphical view]

PANTHER

PTHR10003. PTHR10003. 1 hit.

Pfam

PF00080. Sod_Cu. 1 hit.
[Graphical view]

PRINTS

PR00068. CUZNDISMTASE.

SUPFAM

SSF49329. SOD_Cu_Zn. 1 hit.

PROSITE

PS00087. SOD_CU_ZN_1. 1 hit.
PS00332. SOD_CU_ZN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00445.

NextBio

974334.

Entry information

Entry name

SODC_YEAST

Accession

Primary (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:	May 29, 2013
This is version 162 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program