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P32397

- PPOX_BACSU

UniProt

P32397 - PPOX_BACSU

Protein

Protoporphyrinogen oxidase

Gene

hemY

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 116 (01 Oct 2014)
      Sequence version 1 (01 Oct 1993)
      Previous versions | rss
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    Functioni

    Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. Also oxidizes the pathway intermediate coproporphyrinogen-III.3 Publications

    Catalytic activityi

    Protoporphyrinogen-IX + 3 O2 = protoporphyrin-IX + 3 H2O2.3 Publications

    Cofactori

    Binds 1 FAD per subunit.2 Publications

    Enzyme regulationi

    Only weakly inhibited by acifluorfen, in contrast to eukaryotic family members.2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei49 – 491FAD; via amide nitrogen1 Publication
    Binding sitei409 – 4091FAD1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi12 – 176FAD1 Publication
    Nucleotide bindingi41 – 422FAD1 Publication
    Nucleotide bindingi63 – 664FAD1 Publication
    Nucleotide bindingi448 – 4503FAD1 Publication

    GO - Molecular functioni

    1. oxygen-dependent protoporphyrinogen oxidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Porphyrin biosynthesis

    Keywords - Ligandi

    FAD, Flavoprotein

    Enzyme and pathway databases

    BioCyciBSUB:BSU10140-MONOMER.
    MetaCyc:BSU10140-MONOMER.
    BRENDAi1.3.3.4. 700.
    SABIO-RKP32397.
    UniPathwayiUPA00251; UER00324.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protoporphyrinogen oxidase (EC:1.3.3.4)
    Short name:
    PPO
    Gene namesi
    Name:hemY
    Synonyms:hemG
    Ordered Locus Names:BSU10140
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU10140. [Micado]

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi64 – 641P → A: Decreased affinity for protoporphyrinogen-IX. 1 Publication
    Mutagenesisi71 – 711K → A: Strongly decreased catalytic activity. 1 Publication
    Mutagenesisi176 – 1761I → A: Strongly decreased catalytic activity. 1 Publication
    Mutagenesisi227 – 2271F → R: Decreased affinity for protoporphyrinogen-IX. 1 Publication
    Mutagenesisi366 – 3661Y → A or H: Reduces enzyme activity by 90%. 1 Publication
    Mutagenesisi366 – 3661Y → E: Reduces enzyme activity by 99%. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 470470Protoporphyrinogen oxidasePRO_0000135263Add
    BLAST

    Proteomic databases

    PaxDbiP32397.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    STRINGi224308.BSU10140.

    Structurei

    Secondary structure

    1
    470
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 116
    Helixi15 – 2814
    Turni29 – 324
    Beta strandi34 – 407
    Beta strandi42 – 465
    Beta strandi60 – 634
    Helixi73 – 808
    Beta strandi87 – 893
    Beta strandi95 – 984
    Beta strandi103 – 1053
    Helixi133 – 1408
    Beta strandi145 – 1484
    Helixi152 – 1598
    Helixi162 – 1676
    Helixi169 – 1757
    Turni181 – 1833
    Helixi186 – 1894
    Helixi191 – 1933
    Beta strandi227 – 2304
    Helixi235 – 2439
    Beta strandi247 – 2515
    Beta strandi256 – 2616
    Beta strandi263 – 27311
    Beta strandi275 – 2839
    Helixi287 – 2937
    Turni294 – 2963
    Helixi300 – 3045
    Beta strandi307 – 32014
    Beta strandi329 – 3346
    Beta strandi341 – 3477
    Helixi348 – 3514
    Helixi353 – 3553
    Beta strandi361 – 3677
    Helixi374 – 3763
    Helixi380 – 39112
    Helixi392 – 3943
    Beta strandi402 – 41514
    Helixi420 – 43415
    Beta strandi438 – 4403
    Turni443 – 4453
    Helixi450 – 46819

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3I6DX-ray2.90A/B1-470[»]
    ProteinModelPortaliP32397.
    SMRiP32397. Positions 5-470.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP32397.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the protoporphyrinogen oxidase family.Curated

    Phylogenomic databases

    eggNOGiCOG1232.
    HOGENOMiHOG000269480.
    KOiK00231.
    OMAiWIRSIRG.
    OrthoDBiEOG6RFZTN.
    PhylomeDBiP32397.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.660.20. 1 hit.
    InterProiIPR002937. Amino_oxidase.
    IPR016040. NAD(P)-bd_dom.
    IPR027418. PPOX_C.
    IPR004572. Protoporphyrinogen_oxidase.
    [Graphical view]
    PfamiPF01593. Amino_oxidase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00562. proto_IX_ox. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P32397-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSDGKKHVVI IGGGITGLAA AFYMEKEIKE KNLPLELTLV EASPRVGGKI    50
    QTVKKDGYII ERGPDSFLER KKSAPQLVKD LGLEHLLVNN ATGQSYVLVN 100
    RTLHPMPKGA VMGIPTKIAP FVSTGLFSLS GKARAAMDFI LPASKTKDDQ 150
    SLGEFFRRRV GDEVVENLIE PLLSGIYAGD IDKLSLMSTF PQFYQTEQKH 200
    RSLILGMKKT RPQGSGQQLT AKKQGQFQTL STGLQTLVEE IEKQLKLTKV 250
    YKGTKVTKLS HSGSCYSLEL DNGVTLDADS VIVTAPHKAA AGMLSELPAI 300
    SHLKNMHSTS VANVALGFPE GSVQMEHEGT GFVISRNSDF AITACTWTNK 350
    KWPHAAPEGK TLLRAYVGKA GDESIVDLSD NDIINIVLED LKKVMNINGE 400
    PEMTCVTRWH ESMPQYHVGH KQRIKELREA LASAYPGVYM TGASFEGVGI 450
    PDCIDQGKAA VSDALTYLFS 470
    Length:470
    Mass (Da):51,203
    Last modified:October 1, 1993 - v1
    Checksum:i95CC4E5847686D2E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M97208 Genomic DNA. Translation: AAA22519.1.
    Y14083 Genomic DNA. Translation: CAA74520.1.
    AL009126 Genomic DNA. Translation: CAB12854.1.
    PIRiD47045.
    RefSeqiNP_388895.1. NC_000964.3.
    WP_003245394.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB12854; CAB12854; BSU10140.
    GeneIDi936311.
    KEGGibsu:BSU10140.
    PATRICi18973726. VBIBacSub10457_1057.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M97208 Genomic DNA. Translation: AAA22519.1 .
    Y14083 Genomic DNA. Translation: CAA74520.1 .
    AL009126 Genomic DNA. Translation: CAB12854.1 .
    PIRi D47045.
    RefSeqi NP_388895.1. NC_000964.3.
    WP_003245394.1. NZ_CM000487.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3I6D X-ray 2.90 A/B 1-470 [» ]
    ProteinModelPortali P32397.
    SMRi P32397. Positions 5-470.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU10140.

    Chemistry

    ChEMBLi CHEMBL1075048.

    Proteomic databases

    PaxDbi P32397.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB12854 ; CAB12854 ; BSU10140 .
    GeneIDi 936311.
    KEGGi bsu:BSU10140.
    PATRICi 18973726. VBIBacSub10457_1057.

    Organism-specific databases

    GenoListi BSU10140. [Micado ]

    Phylogenomic databases

    eggNOGi COG1232.
    HOGENOMi HOG000269480.
    KOi K00231.
    OMAi WIRSIRG.
    OrthoDBi EOG6RFZTN.
    PhylomeDBi P32397.

    Enzyme and pathway databases

    UniPathwayi UPA00251 ; UER00324 .
    BioCyci BSUB:BSU10140-MONOMER.
    MetaCyc:BSU10140-MONOMER.
    BRENDAi 1.3.3.4. 700.
    SABIO-RK P32397.

    Miscellaneous databases

    EvolutionaryTracei P32397.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    3.90.660.20. 1 hit.
    InterProi IPR002937. Amino_oxidase.
    IPR016040. NAD(P)-bd_dom.
    IPR027418. PPOX_C.
    IPR004572. Protoporphyrinogen_oxidase.
    [Graphical view ]
    Pfami PF01593. Amino_oxidase. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00562. proto_IX_ox. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes."
      Hansson M., Hederstedt L.
      J. Bacteriol. 174:8081-8093(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus subtilis chromosome contains several dysfunctional genes, the glyB marker, many genes encoding transporter proteins, and the ubiquitous hit gene."
      Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H., Venema G., Bron S.
      Microbiology 144:859-875(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Expression of a cloned protoporphyrinogen oxidase."
      Dailey T.A., Meissner P., Dailey H.A.
      J. Biol. Chem. 269:813-815(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, SUBUNIT, SUBCELLULAR LOCATION, COFACTOR.
    5. "Site-directed mutagenesis and computational study of the Y366 active site in Bacillus subtilis protoporphyrinogen oxidase."
      Sun L., Wen X., Tan Y., Li H., Yang X., Zhao Y., Wang B., Cao Q., Niu C., Xi Z.
      Amino Acids 37:523-530(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF TYR-366, FUNCTION, CATALYTIC ACTIVITY.
    6. "Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis."
      Qin X., Sun L., Wen X., Yang X., Tan Y., Jin H., Cao Q., Zhou W., Xi Z., Shen Y.
      J. Struct. Biol. 170:76-82(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH FAD AND THE INHIBITOR ACIFLUORFEN, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, MUTAGENESIS OF PRO-64; LYS-71; ILE-176 AND PHE-227, SUBUNIT.

    Entry informationi

    Entry nameiPPOX_BACSU
    AccessioniPrimary (citable) accession number: P32397
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: October 1, 2014
    This is version 116 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3