ID   SODF_ECOLI              Reviewed;         193 AA.
AC   P0AGD3; P09157;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   27-MAR-2024, entry version 132.
DE   RecName: Full=Superoxide dismutase [Fe];
DE            EC=1.15.1.1 {ECO:0000269|PubMed:9125513};
GN   Name=sodB; OrderedLocusNames=b1656, JW1648;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 30-35; 44-57 AND
RP   79-116.
RC   STRAIN=K12;
RX   PubMed=2447093; DOI=10.1016/s0021-9258(19)57340-9;
RA   Carlioz A., Ludwig M.L., Stallings W.C., Fee J.A., Steinman H.M.,
RA   Touati D.;
RT   "Iron superoxide dismutase. Nucleotide sequence of the gene from
RT   Escherichia coli K12 and correlations with crystal structures.";
RL   J. Biol. Chem. 263:1555-1562(1988).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA   Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA   Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA   Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA   Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA   Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA   Wada C., Yamamoto Y., Horiuchi T.;
RT   "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT   the 28.0-40.1 min region on the linkage map.";
RL   DNA Res. 3:363-377(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   PROTEIN SEQUENCE OF 2-193.
RX   PubMed=3305077; DOI=10.1016/0014-5793(87)80357-5;
RA   Schinina M.E., Maffey L., Barra D., Bossa F., Puget K., Michelson A.M.;
RT   "The primary structure of iron superoxide dismutase from Escherichia
RT   coli.";
RL   FEBS Lett. 221:87-90(1987).
RN   [6]
RP   PROTEIN SEQUENCE OF 2-30.
RX   PubMed=4590170; DOI=10.1073/pnas.70.12.3725;
RA   Steinman H.M., Hill R.L.;
RT   "Sequence homologies among bacterial and mitochondrial superoxide
RT   dismutases.";
RL   Proc. Natl. Acad. Sci. U.S.A. 70:3725-3729(1973).
RN   [7]
RP   PROTEIN SEQUENCE OF 2-13.
RC   STRAIN=K12 / EMG2;
RX   PubMed=9298646; DOI=10.1002/elps.1150180807;
RA   Link A.J., Robison K., Church G.M.;
RT   "Comparing the predicted and observed properties of proteins encoded in the
RT   genome of Escherichia coli K-12.";
RL   Electrophoresis 18:1259-1313(1997).
RN   [8]
RP   PROTEIN SEQUENCE OF 2-5.
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=9600841; DOI=10.1006/jmbi.1998.1726;
RA   Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C.,
RA   Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L.,
RA   Hochstrasser D.F.;
RT   "Protein identification with N and C-terminal sequence tags in proteome
RT   projects.";
RL   J. Mol. Biol. 278:599-608(1998).
RN   [9]
RP   CATALYTIC ACTIVITY, AND COFACTOR.
RX   PubMed=9125513; DOI=10.1021/bi963047z;
RA   Sorkin D.L., Miller A.-F.;
RT   "Spectroscopic measurement of a long-predicted active site pK in iron-
RT   superoxide dismutase from Escherichia coli.";
RL   Biochemistry 36:4916-4924(1997).
RN   [10]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [11]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-51, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RC   STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX   PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA   Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA   Grishin N.V., Zhao Y.;
RT   "Lysine acetylation is a highly abundant and evolutionarily conserved
RT   modification in Escherichia coli.";
RL   Mol. Cell. Proteomics 8:215-225(2009).
RN   [12]
RP   INDUCTION.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=21289064; DOI=10.1101/gad.2001711;
RA   Prevost K., Desnoyers G., Jacques J.F., Lavoie F., Masse E.;
RT   "Small RNA-induced mRNA degradation achieved through both translation block
RT   and activated cleavage.";
RL   Genes Dev. 25:385-396(2011).
RN   [13]
RP   INDUCTION.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=34210798; DOI=10.1073/pnas.2106964118;
RA   Chen J., To L., de Mets F., Luo X., Majdalani N., Tai C.H., Gottesman S.;
RT   "A fluorescence-based genetic screen reveals diverse mechanisms silencing
RT   small RNA signaling in E. coli.";
RL   Proc. Natl. Acad. Sci. U.S.A. 118:0-0(2021).
RN   [14]
RP   X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH IRON ION, AND
RP   SUBUNIT.
RX   PubMed=6346322; DOI=10.1073/pnas.80.13.3884;
RA   Stallings W.C., Powers T.B., Pattridge K.A., Fee J.A., Ludwig M.L.;
RT   "Iron superoxide dismutase from Escherichia coli at 3.1-A resolution: a
RT   structure unlike that of copper/zinc protein at both monomer and dimer
RT   levels.";
RL   Proc. Natl. Acad. Sci. U.S.A. 80:3884-3888(1983).
CC   -!- FUNCTION: Destroys superoxide anion radicals which are normally
CC       produced within the cells and which are toxic to biological systems.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 H(+) + 2 superoxide = H2O2 + O2; Xref=Rhea:RHEA:20696,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC         ChEBI:CHEBI:18421; EC=1.15.1.1;
CC         Evidence={ECO:0000269|PubMed:9125513};
CC   -!- COFACTOR:
CC       Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC         Evidence={ECO:0000269|PubMed:9125513};
CC       Note=Binds 1 Fe cation per subunit. {ECO:0000269|PubMed:9125513};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:6346322}.
CC   -!- INDUCTION: The transcript is subject to small RNA (sRNA)-mediated
CC       degradation; sRNA RyhB-binding at the ribosome-binding site (RBS) both
CC       blocks translation and induces mRNA cleavage by the RNA degradosome
CC       over 350 bases downstream. RhyB blocks translation even in the absence
CC       of the RNA degradosome (PubMed:21289064). Deletion of fur derepresses
CC       rhyB expression, and leads to less expression of this gene
CC       (PubMed:34210798). {ECO:0000269|PubMed:21289064,
CC       ECO:0000269|PubMed:34210798}.
CC   -!- SIMILARITY: Belongs to the iron/manganese superoxide dismutase family.
CC       {ECO:0000305}.
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DR   EMBL; J03511; AAA24637.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC74728.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA15422.1; -; Genomic_DNA.
DR   PIR; A29940; DSECF.
DR   RefSeq; NP_416173.1; NC_000913.3.
DR   RefSeq; WP_000007283.1; NZ_STEB01000003.1.
DR   PDB; 1ISA; X-ray; 1.80 A; A/B=2-193.
DR   PDB; 1ISB; X-ray; 1.85 A; A/B=2-193.
DR   PDB; 1ISC; X-ray; 1.80 A; A/B=2-193.
DR   PDB; 1ZA5; X-ray; 1.80 A; A/B=2-193.
DR   PDB; 2BKB; X-ray; 1.70 A; A/B/C/D=2-193.
DR   PDB; 2NYB; X-ray; 1.10 A; A/B/C/D=2-193.
DR   PDBsum; 1ISA; -.
DR   PDBsum; 1ISB; -.
DR   PDBsum; 1ISC; -.
DR   PDBsum; 1ZA5; -.
DR   PDBsum; 2BKB; -.
DR   PDBsum; 2NYB; -.
DR   AlphaFoldDB; P0AGD3; -.
DR   BMRB; P0AGD3; -.
DR   SMR; P0AGD3; -.
DR   BioGRID; 4260265; 63.
DR   IntAct; P0AGD3; 6.
DR   STRING; 511145.b1656; -.
DR   iPTMnet; P0AGD3; -.
DR   jPOST; P0AGD3; -.
DR   PaxDb; 511145-b1656; -.
DR   EnsemblBacteria; AAC74728; AAC74728; b1656.
DR   GeneID; 75204501; -.
DR   GeneID; 944953; -.
DR   KEGG; ecj:JW1648; -.
DR   KEGG; eco:b1656; -.
DR   PATRIC; fig|1411691.4.peg.602; -.
DR   EchoBASE; EB0947; -.
DR   eggNOG; COG0605; Bacteria.
DR   HOGENOM; CLU_031625_0_0_6; -.
DR   InParanoid; P0AGD3; -.
DR   OMA; DSLINWD; -.
DR   OrthoDB; 9803125at2; -.
DR   PhylomeDB; P0AGD3; -.
DR   BioCyc; EcoCyc:SUPEROX-DISMUTFE-MONOMER; -.
DR   BioCyc; MetaCyc:SUPEROX-DISMUTFE-MONOMER; -.
DR   BRENDA; 1.15.1.1; 2026.
DR   EvolutionaryTrace; P0AGD3; -.
DR   PRO; PR:P0AGD3; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR   GO; GO:0005829; C:cytosol; HDA:UniProtKB.
DR   GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR   GO; GO:0005506; F:iron ion binding; IDA:EcoCyc.
DR   GO; GO:0016491; F:oxidoreductase activity; IDA:EcoliWiki.
DR   GO; GO:0004784; F:superoxide dismutase activity; IDA:EcoliWiki.
DR   GO; GO:0019430; P:removal of superoxide radicals; IDA:EcoliWiki.
DR   GO; GO:0000303; P:response to superoxide; IDA:EcoliWiki.
DR   GO; GO:0006801; P:superoxide metabolic process; IDA:EcoliWiki.
DR   Gene3D; 1.10.287.990; Fe,Mn superoxide dismutase (SOD) domain; 1.
DR   Gene3D; 3.55.40.20; Iron/manganese superoxide dismutase, C-terminal domain; 1.
DR   InterPro; IPR001189; Mn/Fe_SOD.
DR   InterPro; IPR019833; Mn/Fe_SOD_BS.
DR   InterPro; IPR019832; Mn/Fe_SOD_C.
DR   InterPro; IPR019831; Mn/Fe_SOD_N.
DR   InterPro; IPR036324; Mn/Fe_SOD_N_sf.
DR   InterPro; IPR036314; SOD_C_sf.
DR   PANTHER; PTHR42769; SUPEROXIDE DISMUTASE; 1.
DR   PANTHER; PTHR42769:SF3; SUPEROXIDE DISMUTASE [FE] 2, CHLOROPLASTIC; 1.
DR   Pfam; PF02777; Sod_Fe_C; 1.
DR   Pfam; PF00081; Sod_Fe_N; 1.
DR   PIRSF; PIRSF000349; SODismutase; 1.
DR   PRINTS; PR01703; MNSODISMTASE.
DR   SUPFAM; SSF54719; Fe,Mn superoxide dismutase (SOD), C-terminal domain; 1.
DR   SUPFAM; SSF46609; Fe,Mn superoxide dismutase (SOD), N-terminal domain; 1.
DR   PROSITE; PS00088; SOD_MN; 1.
DR   SWISS-2DPAGE; P0AGD3; -.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Direct protein sequencing; Iron; Metal-binding;
KW   Oxidoreductase; Reference proteome.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:3305077,
FT                   ECO:0000269|PubMed:4590170, ECO:0000269|PubMed:9298646,
FT                   ECO:0000269|PubMed:9600841"
FT   CHAIN           2..193
FT                   /note="Superoxide dismutase [Fe]"
FT                   /id="PRO_0000159979"
FT   BINDING         27
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT   BINDING         74
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT   BINDING         157
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT   BINDING         161
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT   MOD_RES         51
FT                   /note="N6-acetyllysine"
FT                   /evidence="ECO:0000269|PubMed:18723842"
FT   TURN            12..18
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           21..29
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           31..43
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   TURN            47..50
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           53..57
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           62..79
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           91..101
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           104..117
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   STRAND          120..128
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   STRAND          134..140
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           145..147
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   STRAND          151..157
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           160..162
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           164..167
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           171..179
FT                   /evidence="ECO:0007829|PDB:2NYB"
FT   HELIX           184..192
FT                   /evidence="ECO:0007829|PDB:2NYB"
SQ   SEQUENCE   193 AA;  21266 MW;  91236D2A8FE61474 CRC64;
     MSFELPALPY AKDALAPHIS AETIEYHYGK HHQTYVTNLN NLIKGTAFEG KSLEEIIRSS
     EGGVFNNAAQ VWNHTFYWNC LAPNAGGEPT GKVAEAIAAS FGSFADFKAQ FTDAAIKNFG
     SGWTWLVKNS DGKLAIVSTS NAGTPLTTDA TPLLTVDVWE HAYYIDYRNA RPGYLEHFWA
     LVNWEFVAKN LAA
//