SODF_PORGI
ID SODF_PORGI Reviewed; 191 AA.
AC P19665;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1991, sequence version 2.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Superoxide dismutase [Mn/Fe];
DE EC=1.15.1.1 {ECO:0000305|PubMed:2307656};
GN Name=sodB; Synonyms=sod {ECO:0000303|PubMed:1840572};
GN OrderedLocusNames=PG_1545;
OS Porphyromonas gingivalis (strain ATCC BAA-308 / W83).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae;
OC Porphyromonas.
OX NCBI_TaxID=242619;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2265754; DOI=10.1016/0378-1119(90)90357-w;
RA Nakayama K.;
RT "The superoxide dismutase-encoding gene of the obligately anaerobic
RT bacterium Bacteroides gingivalis.";
RL Gene 96:149-150(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 53977;
RX PubMed=1840572; DOI=10.1128/iai.59.4.1564-1566.1991;
RA Choi J.I., Takahashi N., Kato T., Kuramitsu H.K.;
RT "Isolation, expression, and nucleotide sequence of the sod gene from
RT Porphyromonas gingivalis.";
RL Infect. Immun. 59:1564-1566(1991).
RN [3]
RP PROTEIN SEQUENCE.
RC STRAIN=381;
RX PubMed=2226833; DOI=10.1016/0014-5793(90)80488-5;
RA Amano A., Shizukuishi S., Tsunemitsu A., Maekawa K., Tsunasawa S.;
RT "The primary structure of superoxide dismutase purified from anaerobically
RT maintained Bacteroides gingivalis.";
RL FEBS Lett. 272:217-220(1990).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-308 / W83;
RX PubMed=12949112; DOI=10.1128/jb.185.18.5591-5601.2003;
RA Nelson K.E., Fleischmann R.D., DeBoy R.T., Paulsen I.T., Fouts D.E.,
RA Eisen J.A., Daugherty S.C., Dodson R.J., Durkin A.S., Gwinn M.L.,
RA Haft D.H., Kolonay J.F., Nelson W.C., Mason T.M., Tallon L., Gray J.,
RA Granger D., Tettelin H., Dong H., Galvin J.L., Duncan M.J., Dewhirst F.E.,
RA Fraser C.M.;
RT "Complete genome sequence of the oral pathogenic bacterium Porphyromonas
RT gingivalis strain W83.";
RL J. Bacteriol. 185:5591-5601(2003).
RN [5]
RP PROTEIN SEQUENCE OF 1-12, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY
RP REGULATION, AND SUBUNIT.
RC STRAIN=381;
RX PubMed=2307656; DOI=10.1128/jb.172.3.1457-1463.1990;
RA Amano A., Shizukuishi S., Tamagawa H., Iwakura K., Tsunasawa S.,
RA Tsunemitsu A.;
RT "Characterization of superoxide dismutases purified from either
RT anaerobically maintained or aerated Bacteroides gingivalis.";
RL J. Bacteriol. 172:1457-1463(1990).
RN [6] {ECO:0007744|PDB:1QNN}
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH IRON, AND COFACTOR.
RX PubMed=10848964; DOI=10.1046/j.1432-1327.2000.01373.x;
RA Sugio S., Hiraoka B.Y., Yamakura F.;
RT "Crystal structure of cambialistic superoxide dismutase from Porphyromonas
RT gingivalis.";
RL Eur. J. Biochem. 267:3487-3495(2000).
RN [7] {ECO:0007744|PDB:1UER, ECO:0007744|PDB:1UES}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT THR-155 IN
RP COMPLEX WITH IRON OR MANGANESE, COFACTOR, AND MUTAGENESIS OF GLY-155.
RX PubMed=12962504; DOI=10.1021/bi0349625;
RA Yamakura F., Sugio S., Hiraoka B.Y., Ohmori D., Yokota T.;
RT "Pronounced conversion of the metal-specific activity of superoxide
RT dismutase from Porphyromonas gingivalis by the mutation of a single amino
RT acid (Gly155Thr) located apart from the active site.";
RL Biochemistry 42:10790-10799(2003).
CC -!- FUNCTION: Destroys superoxide anion radicals which are normally
CC produced within the cells and which are toxic to biological systems.
CC Catalyzes the dismutation of superoxide anion radicals into O2 and H2O2
CC by successive reduction and oxidation of the transition metal ion at
CC the active site.
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:0000305|PubMed:2307656};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:20697;
CC Evidence={ECO:0000305|PubMed:2307656};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:10848964, ECO:0000269|PubMed:2307656};
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Evidence={ECO:0000269|PubMed:10848964, ECO:0000269|PubMed:12962504,
CC ECO:0000269|PubMed:2307656};
CC Note=Binds 1 Mn(2+) or Fe(3+) ion per subunit.
CC {ECO:0000269|PubMed:10848964, ECO:0000269|PubMed:12962504};
CC -!- ACTIVITY REGULATION: Inhibited by hydrogen peroxide.
CC {ECO:0000269|PubMed:2307656}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:2307656}.
CC -!- SIMILARITY: Belongs to the iron/manganese superoxide dismutase family.
CC {ECO:0000305}.
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DR EMBL; D90152; BAA14182.1; -; Genomic_DNA.
DR EMBL; M60401; AAA25651.1; -; Genomic_DNA.
DR EMBL; AE015924; AAQ66583.1; -; Genomic_DNA.
DR PIR; A43585; A43585.
DR RefSeq; WP_004585361.1; NC_002950.2.
DR PDB; 1QNN; X-ray; 1.80 A; A/B/C/D=1-191.
DR PDB; 1UER; X-ray; 1.60 A; A/B/C/D=1-191.
DR PDB; 1UES; X-ray; 1.60 A; A/B/C/D=1-191.
DR PDBsum; 1QNN; -.
DR PDBsum; 1UER; -.
DR PDBsum; 1UES; -.
DR AlphaFoldDB; P19665; -.
DR SMR; P19665; -.
DR STRING; 242619.PG_1545; -.
DR EnsemblBacteria; AAQ66583; AAQ66583; PG_1545.
DR GeneID; 29255789; -.
DR KEGG; pgi:PG_1545; -.
DR eggNOG; COG0605; Bacteria.
DR HOGENOM; CLU_031625_0_0_10; -.
DR OMA; YEGWKGE; -.
DR OrthoDB; 1440645at2; -.
DR EvolutionaryTrace; P19665; -.
DR Proteomes; UP000000588; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004784; F:superoxide dismutase activity; IEA:UniProtKB-EC.
DR Gene3D; 1.10.287.990; -; 1.
DR Gene3D; 3.55.40.20; -; 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 Pfam; PF02777; Sod_Fe_C; 1.
DR Pfam; PF00081; Sod_Fe_N; 1.
DR PIRSF; PIRSF000349; SODismutase; 1.
DR PRINTS; PR01703; MNSODISMTASE.
DR SUPFAM; SSF46609; SSF46609; 1.
DR SUPFAM; SSF54719; SSF54719; 1.
DR PROSITE; PS00088; SOD_MN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Iron; Manganese; Metal-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..191
FT /note="Superoxide dismutase [Mn/Fe]"
FT /id="PRO_0000159993"
FT BINDING 27
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1QNN, ECO:0007744|PDB:1UER"
FT BINDING 27
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1UES"
FT BINDING 74
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1QNN, ECO:0007744|PDB:1UER"
FT BINDING 74
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1UES"
FT BINDING 157
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1QNN, ECO:0007744|PDB:1UER"
FT BINDING 157
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1UES"
FT BINDING 161
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1QNN, ECO:0007744|PDB:1UER"
FT BINDING 161
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:12962504,
FT ECO:0007744|PDB:1UES"
FT MUTAGEN 155
FT /note="G->T: Converts the metal-specific activity of the
FT enzyme from a cambialistic type (showing the same activity
FT with Fe and Mn) to an Fe-specific type."
FT /evidence="ECO:0000269|PubMed:12962504"
FT CONFLICT 13
FT /note="D -> Y (in Ref. 2; AAA25651)"
FT /evidence="ECO:0000305"
FT CONFLICT 29
FT /note="G -> E (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 112
FT /note="N -> D (in Ref. 2; AAA25651)"
FT /evidence="ECO:0000305"
FT TURN 12..19
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 21..27
FT /evidence="ECO:0007829|PDB:1UER"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 31..42
FT /evidence="ECO:0007829|PDB:1UER"
FT TURN 43..45
FT /evidence="ECO:0007829|PDB:1UER"
FT TURN 47..50
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 53..59
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 62..79
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 91..101
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:1UER"
FT STRAND 120..128
FT /evidence="ECO:0007829|PDB:1UER"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:1UER"
FT STRAND 151..157
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 171..178
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:1UER"
FT HELIX 184..190
FT /evidence="ECO:0007829|PDB:1UER"
SQ SEQUENCE 191 AA; 21501 MW; AA53419397BF6BA1 CRC64;
MTHELISLPY AVDALAPVIS KETVEFHHGK HLKTYVDNLN KLIIGTEFEN ADLNTIVQKS
EGGIFNNAGQ TLNHNLYFTQ FRPGKGGAPK GKLGEAIDKQ FGSFEKFKEE FNTAGTTLFG
SGWVWLASDA NGKLSIEKEP NAGNPVRKGL NPLLGFDVWE HAYYLTYQNR RADHLKDLWS
IVDWDIVESR Y
