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P32397

- PPOX_BACSU

UniProt

P32397 - PPOX_BACSU

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Protein

Protoporphyrinogen oxidase

Gene

hemY

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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

FAD2 PublicationsNote: 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
Complete GO annotation...

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-KW
Complete GO annotation...

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP32397.
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

        10         20         30         40         50
MSDGKKHVVI IGGGITGLAA AFYMEKEIKE KNLPLELTLV EASPRVGGKI
60 70 80 90 100
QTVKKDGYII ERGPDSFLER KKSAPQLVKD LGLEHLLVNN ATGQSYVLVN
110 120 130 140 150
RTLHPMPKGA VMGIPTKIAP FVSTGLFSLS GKARAAMDFI LPASKTKDDQ
160 170 180 190 200
SLGEFFRRRV GDEVVENLIE PLLSGIYAGD IDKLSLMSTF PQFYQTEQKH
210 220 230 240 250
RSLILGMKKT RPQGSGQQLT AKKQGQFQTL STGLQTLVEE IEKQLKLTKV
260 270 280 290 300
YKGTKVTKLS HSGSCYSLEL DNGVTLDADS VIVTAPHKAA AGMLSELPAI
310 320 330 340 350
SHLKNMHSTS VANVALGFPE GSVQMEHEGT GFVISRNSDF AITACTWTNK
360 370 380 390 400
KWPHAAPEGK TLLRAYVGKA GDESIVDLSD NDIINIVLED LKKVMNINGE
410 420 430 440 450
PEMTCVTRWH ESMPQYHVGH KQRIKELREA LASAYPGVYM TGASFEGVGI
460 470
PDCIDQGKAA VSDALTYLFS
Length:470
Mass (Da):51,203
Last modified:October 1, 1993 - v1
Checksum:i95CC4E5847686D2E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

BindingDBi P32397.
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.
InParanoidi P32397.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 118 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