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P32397 (PPOX_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 112. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protoporphyrinogen oxidase

Short name=PPO
EC=1.3.3.4
Gene names
Name:hemY
Synonyms:hemG
Ordered Locus Names:BSU10140
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length470 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. Also oxidizes the pathway intermediate coproporphyrinogen-III. Ref.4 Ref.5 Ref.6

Catalytic activity

Protoporphyrinogen-IX + 3 O2 = protoporphyrin-IX + 3 H2O2. Ref.4 Ref.5 Ref.6

Cofactor

Binds 1 FAD per subunit. Ref.4 Ref.6

Enzyme regulation

Only weakly inhibited by acifluorfen, in contrast to eukaryotic family members. Ref.4 Ref.6

Pathway

Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrin-IX from protoporphyrinogen-IX: step 1/1.

Subunit structure

Monomer. Ref.4 Ref.6

Subcellular location

Cytoplasm Ref.4.

Sequence similarities

Belongs to the protoporphyrinogen oxidase family.

Ontologies

Keywords
   Biological processPorphyrin biosynthesis
   Cellular componentCytoplasm
   LigandFAD
Flavoprotein
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processprotoporphyrinogen IX biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionoxygen-dependent protoporphyrinogen oxidase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 470470Protoporphyrinogen oxidase
PRO_0000135263

Regions

Nucleotide binding12 – 176FAD
Nucleotide binding41 – 422FAD
Nucleotide binding63 – 664FAD
Nucleotide binding448 – 4503FAD

Sites

Binding site491FAD; via amide nitrogen
Binding site4091FAD

Experimental info

Mutagenesis641P → A: Decreased affinity for protoporphyrinogen-IX. Ref.6
Mutagenesis711K → A: Strongly decreased catalytic activity. Ref.6
Mutagenesis1761I → A: Strongly decreased catalytic activity. Ref.6
Mutagenesis2271F → R: Decreased affinity for protoporphyrinogen-IX. Ref.6
Mutagenesis3661Y → A or H: Reduces enzyme activity by 90%. Ref.5
Mutagenesis3661Y → E: Reduces enzyme activity by 99%. Ref.5

Secondary structure

............................................................................... 470
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P32397 [UniParc].

Last modified October 1, 1993. Version 1.
Checksum: 95CC4E5847686D2E

FASTA47051,203
        10         20         30         40         50         60 
MSDGKKHVVI IGGGITGLAA AFYMEKEIKE KNLPLELTLV EASPRVGGKI QTVKKDGYII 

        70         80         90        100        110        120 
ERGPDSFLER KKSAPQLVKD LGLEHLLVNN ATGQSYVLVN RTLHPMPKGA VMGIPTKIAP 

       130        140        150        160        170        180 
FVSTGLFSLS GKARAAMDFI LPASKTKDDQ SLGEFFRRRV GDEVVENLIE PLLSGIYAGD 

       190        200        210        220        230        240 
IDKLSLMSTF PQFYQTEQKH RSLILGMKKT RPQGSGQQLT AKKQGQFQTL STGLQTLVEE 

       250        260        270        280        290        300 
IEKQLKLTKV YKGTKVTKLS HSGSCYSLEL DNGVTLDADS VIVTAPHKAA AGMLSELPAI 

       310        320        330        340        350        360 
SHLKNMHSTS VANVALGFPE GSVQMEHEGT GFVISRNSDF AITACTWTNK KWPHAAPEGK 

       370        380        390        400        410        420 
TLLRAYVGKA GDESIVDLSD NDIINIVLED LKKVMNINGE PEMTCVTRWH ESMPQYHVGH 

       430        440        450        460        470 
KQRIKELREA LASAYPGVYM TGASFEGVGI PDCIDQGKAA VSDALTYLFS 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M97208 Genomic DNA. Translation: AAA22519.1.
Y14083 Genomic DNA. Translation: CAA74520.1.
AL009126 Genomic DNA. Translation: CAB12854.1.
PIRD47045.
RefSeqNP_388895.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3I6DX-ray2.90A/B1-470[»]
ProteinModelPortalP32397.
SMRP32397. Positions 5-470.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU10140.

Chemistry

ChEMBLCHEMBL1075048.

Proteomic databases

PaxDbP32397.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB12854; CAB12854; BSU10140.
GeneID936311.
KEGGbsu:BSU10140.
PATRIC18973726. VBIBacSub10457_1057.

Organism-specific databases

GenoListBSU10140. [Micado]

Phylogenomic databases

eggNOGCOG1232.
HOGENOMHOG000269480.
KOK00231.
OMAPNGFLDS.
OrthoDBEOG6RFZTN.
ProtClustDBPRK11883.

Enzyme and pathway databases

BioCycBSUB:BSU10140-MONOMER.
MetaCyc:BSU10140-MONOMER.
BRENDA1.3.3.4. 700.
SABIO-RKP32397.
UniPathwayUPA00251; UER00324.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
3.90.660.20. 1 hit.
InterProIPR002937. Amino_oxidase.
IPR016040. NAD(P)-bd_dom.
IPR004572. Protoporphyrinogen_oxidase.
IPR027418. Protoporphyrinogen_oxidase_C.
[Graphical view]
PfamPF01593. Amino_oxidase. 1 hit.
[Graphical view]
TIGRFAMsTIGR00562. proto_IX_ox. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP32397.

Entry information

Entry namePPOX_BACSU
AccessionPrimary (citable) accession number: P32397
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: February 19, 2014
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList