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Protein

Superoxide dismutase [Mn/Fe]

Gene

sodB

Organism
Porphyromonas gingivalis (strain ATCC BAA-308 / W83)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.

Catalytic activityi

2 superoxide + 2 H+ = O2 + H2O2.

Cofactori

Mn2+, Fe2+Note: Binds 1 Mn(2+) or Fe2+ ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi27 – 271Manganese or iron
Metal bindingi74 – 741Manganese or iron
Metal bindingi157 – 1571Manganese or iron
Metal bindingi161 – 1611Manganese or iron

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciPGIN242619:GHX8-1394-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Superoxide dismutase [Mn/Fe] (EC:1.15.1.1)
Gene namesi
Name:sodB
Ordered Locus Names:PG_1545
OrganismiPorphyromonas gingivalis (strain ATCC BAA-308 / W83)
Taxonomic identifieri242619 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
ProteomesiUP000000588 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 191191Superoxide dismutase [Mn/Fe]PRO_0000159993Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi242619.PG1545.

Structurei

Secondary structure

1
191
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni12 – 198Combined sources
Helixi21 – 277Combined sources
Turni28 – 303Combined sources
Helixi31 – 4212Combined sources
Turni43 – 453Combined sources
Turni47 – 504Combined sources
Helixi53 – 597Combined sources
Helixi62 – 7918Combined sources
Helixi91 – 10111Combined sources
Helixi104 – 11714Combined sources
Beta strandi120 – 1289Combined sources
Beta strandi134 – 1407Combined sources
Helixi145 – 1484Combined sources
Beta strandi151 – 1577Combined sources
Helixi160 – 1623Combined sources
Helixi164 – 1674Combined sources
Helixi171 – 1788Combined sources
Helixi179 – 1813Combined sources
Helixi184 – 1907Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QNNX-ray1.80A/B/C/D1-191[»]
1UERX-ray1.60A/B/C/D1-191[»]
1UESX-ray1.60A/B/C/D1-191[»]
ProteinModelPortaliP19665.
SMRiP19665. Positions 1-191.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19665.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0605.
KOiK04564.
OMAiQNDRARY.
OrthoDBiEOG63NMNT.

Family and domain databases

InterProiIPR001189. Mn/Fe_SOD.
IPR019833. Mn/Fe_SOD_BS.
IPR019832. Mn/Fe_SOD_C.
IPR019831. Mn/Fe_SOD_N.
[Graphical view]
PANTHERiPTHR11404. PTHR11404. 1 hit.
PfamiPF02777. Sod_Fe_C. 1 hit.
PF00081. Sod_Fe_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000349. SODismutase. 1 hit.
PRINTSiPR01703. MNSODISMTASE.
SUPFAMiSSF46609. SSF46609. 1 hit.
SSF54719. SSF54719. 1 hit.
PROSITEiPS00088. SOD_MN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P19665-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTHELISLPY AVDALAPVIS KETVEFHHGK HLKTYVDNLN KLIIGTEFEN
60 70 80 90 100
ADLNTIVQKS EGGIFNNAGQ TLNHNLYFTQ FRPGKGGAPK GKLGEAIDKQ
110 120 130 140 150
FGSFEKFKEE FNTAGTTLFG SGWVWLASDA NGKLSIEKEP NAGNPVRKGL
160 170 180 190
NPLLGFDVWE HAYYLTYQNR RADHLKDLWS IVDWDIVESR Y
Length:191
Mass (Da):21,501
Last modified:May 1, 1991 - v2
Checksum:iAA53419397BF6BA1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti13 – 131D → Y in AAA25651 (PubMed:1840572).Curated
Sequence conflicti29 – 291G → E AA sequence (PubMed:2226833).Curated
Sequence conflicti112 – 1121N → D in AAA25651 (PubMed:1840572).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D90152 Genomic DNA. Translation: BAA14182.1.
M60401 Genomic DNA. Translation: AAA25651.1.
AE015924 Genomic DNA. Translation: AAQ66583.1.
PIRiA43585.
RefSeqiWP_004585361.1. NC_002950.2.

Genome annotation databases

EnsemblBacteriaiAAQ66583; AAQ66583; PG_1545.
GeneIDi2553021.
KEGGipgi:PG1545.
PATRICi22974068. VBIPorGin26334_0556.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D90152 Genomic DNA. Translation: BAA14182.1.
M60401 Genomic DNA. Translation: AAA25651.1.
AE015924 Genomic DNA. Translation: AAQ66583.1.
PIRiA43585.
RefSeqiWP_004585361.1. NC_002950.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QNNX-ray1.80A/B/C/D1-191[»]
1UERX-ray1.60A/B/C/D1-191[»]
1UESX-ray1.60A/B/C/D1-191[»]
ProteinModelPortaliP19665.
SMRiP19665. Positions 1-191.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi242619.PG1545.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAQ66583; AAQ66583; PG_1545.
GeneIDi2553021.
KEGGipgi:PG1545.
PATRICi22974068. VBIPorGin26334_0556.

Phylogenomic databases

eggNOGiCOG0605.
KOiK04564.
OMAiQNDRARY.
OrthoDBiEOG63NMNT.

Enzyme and pathway databases

BioCyciPGIN242619:GHX8-1394-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP19665.

Family and domain databases

InterProiIPR001189. Mn/Fe_SOD.
IPR019833. Mn/Fe_SOD_BS.
IPR019832. Mn/Fe_SOD_C.
IPR019831. Mn/Fe_SOD_N.
[Graphical view]
PANTHERiPTHR11404. PTHR11404. 1 hit.
PfamiPF02777. Sod_Fe_C. 1 hit.
PF00081. Sod_Fe_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000349. SODismutase. 1 hit.
PRINTSiPR01703. MNSODISMTASE.
SUPFAMiSSF46609. SSF46609. 1 hit.
SSF54719. SSF54719. 1 hit.
PROSITEiPS00088. SOD_MN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The superoxide dismutase-encoding gene of the obligately anaerobic bacterium Bacteroides gingivalis."
    Nakayama K.
    Gene 96:149-150(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Isolation, expression, and nucleotide sequence of the sod gene from Porphyromonas gingivalis."
    Choi J.I., Takahashi N., Kato T., Kuramitsu H.K.
    Infect. Immun. 59:1564-1566(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The primary structure of superoxide dismutase purified from anaerobically maintained Bacteroides gingivalis."
    Amano A., Shizukuishi S., Tsunemitsu A., Maekawa K., Tsunasawa S.
    FEBS Lett. 272:217-220(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE.
    Strain: 381.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-308 / W83.
  5. "Characterization of superoxide dismutases purified from either anaerobically maintained or aerated Bacteroides gingivalis."
    Amano A., Shizukuishi S., Tamagawa H., Iwakura K., Tsunasawa S., Tsunemitsu A.
    J. Bacteriol. 172:1457-1463(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-12.
  6. "Crystal structure of cambialistic superoxide dismutase from Porphyromonas gingivalis."
    Sugio S., Hiraoka B.Y., Yamakura F.
    Eur. J. Biochem. 267:3487-3495(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Entry informationi

Entry nameiSODF_PORGI
AccessioniPrimary (citable) accession number: P19665
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: May 1, 1991
Last modified: July 22, 2015
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3

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 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.