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Protein

Protoporphyrinogen oxidase

Gene

hemY

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: 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: protoporphyrin-IX biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes protoporphyrin-IX from protoporphyrinogen-IX.
Proteins known to be involved in this subpathway in this organism are:
  1. Protoporphyrinogen oxidase (hemY)
This subpathway is part of the pathway protoporphyrin-IX biosynthesis, which is itself part of Porphyrin-containing compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes protoporphyrin-IX from protoporphyrinogen-IX, the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei49FAD; via amide nitrogen1 Publication1
Binding sitei409FAD1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi12 – 17FAD1 Publication6
Nucleotide bindingi41 – 42FAD1 Publication2
Nucleotide bindingi63 – 66FAD1 Publication4
Nucleotide bindingi448 – 450FAD1 Publication3

GO - Molecular functioni

GO - Biological processi

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. 658.
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
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi64P → A: Decreased affinity for protoporphyrinogen-IX. 1 Publication1
Mutagenesisi71K → A: Strongly decreased catalytic activity. 1 Publication1
Mutagenesisi176I → A: Strongly decreased catalytic activity. 1 Publication1
Mutagenesisi227F → R: Decreased affinity for protoporphyrinogen-IX. 1 Publication1
Mutagenesisi366Y → A or H: Reduces enzyme activity by 90%. 1 Publication1
Mutagenesisi366Y → E: Reduces enzyme activity by 99%. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL1075048.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001352631 – 470Protoporphyrinogen oxidaseAdd BLAST470

Proteomic databases

PaxDbiP32397.
PRIDEiP32397.

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005636.

Chemistry databases

BindingDBiP32397.

Structurei

Secondary structure

1470
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 11Combined sources6
Helixi15 – 28Combined sources14
Turni29 – 32Combined sources4
Beta strandi34 – 40Combined sources7
Beta strandi42 – 46Combined sources5
Beta strandi60 – 63Combined sources4
Helixi73 – 80Combined sources8
Beta strandi87 – 89Combined sources3
Beta strandi95 – 98Combined sources4
Beta strandi103 – 105Combined sources3
Helixi133 – 140Combined sources8
Beta strandi145 – 148Combined sources4
Helixi152 – 159Combined sources8
Helixi162 – 167Combined sources6
Helixi169 – 175Combined sources7
Turni181 – 183Combined sources3
Helixi186 – 189Combined sources4
Helixi191 – 193Combined sources3
Beta strandi227 – 230Combined sources4
Helixi235 – 243Combined sources9
Beta strandi247 – 251Combined sources5
Beta strandi256 – 261Combined sources6
Beta strandi263 – 273Combined sources11
Beta strandi275 – 283Combined sources9
Helixi287 – 293Combined sources7
Turni294 – 296Combined sources3
Helixi300 – 304Combined sources5
Beta strandi307 – 320Combined sources14
Beta strandi329 – 334Combined sources6
Beta strandi341 – 347Combined sources7
Helixi348 – 351Combined sources4
Helixi353 – 355Combined sources3
Beta strandi361 – 367Combined sources7
Helixi374 – 376Combined sources3
Helixi380 – 391Combined sources12
Helixi392 – 394Combined sources3
Beta strandi402 – 415Combined sources14
Helixi420 – 434Combined sources15
Beta strandi438 – 440Combined sources3
Turni443 – 445Combined sources3
Helixi450 – 468Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3I6DX-ray2.90A/B1-470[»]
ProteinModelPortaliP32397.
SMRiP32397.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32397.

Family & Domainsi

Sequence similaritiesi

Belongs to the protoporphyrinogen oxidase family.Curated

Phylogenomic databases

eggNOGiENOG4105C1Q. Bacteria.
COG1232. LUCA.
HOGENOMiHOG000269480.
InParanoidiP32397.
KOiK00231.
OMAiDSCCFDM.
PhylomeDBiP32397.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.660.20. 1 hit.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_dom.
IPR016040. NAD(P)-bd_dom.
IPR027418. PPOX_C.
IPR004572. Protoporphyrinogen_oxidase.
[Graphical view]
PfamiPF01593. Amino_oxidase. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 2 hits.
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_JNCM01000035.1.

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.
PIRiD47045.
RefSeqiNP_388895.1. NC_000964.3.
WP_003245394.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3I6DX-ray2.90A/B1-470[»]
ProteinModelPortaliP32397.
SMRiP32397.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005636.

Chemistry databases

BindingDBiP32397.
ChEMBLiCHEMBL1075048.

Proteomic databases

PaxDbiP32397.
PRIDEiP32397.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4105C1Q. Bacteria.
COG1232. LUCA.
HOGENOMiHOG000269480.
InParanoidiP32397.
KOiK00231.
OMAiDSCCFDM.
PhylomeDBiP32397.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00324.
BioCyciBSUB:BSU10140-MONOMER.
MetaCyc:BSU10140-MONOMER.
BRENDAi1.3.3.4. 658.
SABIO-RKP32397.

Miscellaneous databases

EvolutionaryTraceiP32397.
PROiP32397.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.660.20. 1 hit.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_dom.
IPR016040. NAD(P)-bd_dom.
IPR027418. PPOX_C.
IPR004572. Protoporphyrinogen_oxidase.
[Graphical view]
PfamiPF01593. Amino_oxidase. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 2 hits.
TIGRFAMsiTIGR00562. proto_IX_ox. 1 hit.
ProtoNetiSearch...

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 2, 2016
This is version 132 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

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 one 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.