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Protein

Protoporphyrinogen oxidase, mitochondrial

Gene

PPXII

Organism
Nicotiana tabacum (Common tobacco)
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.1 Publication
Provides precursor for the mitochondrial and plastidic heme synthesis and the predominant chlorophyll synthesis in plastids.1 Publication

Catalytic activityi

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

Cofactori

FAD1 PublicationNote: Binds 1 FAD per subunit.1 Publication

Enzyme regulationi

Inhibited by the herbicide acifluorfen.

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, mitochondrial (PPXII), Protoporphyrinogen oxidase, chloroplastic (PPXI)
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 sitei51FAD1 Publication1
Binding sitei264FAD; via amide nitrogen and carbonyl oxygen1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi20 – 25FAD1 Publication6
Nucleotide bindingi43 – 44FAD1 Publication2
Nucleotide bindingi65 – 68FAD1 Publication4
Nucleotide bindingi473 – 475FAD1 Publication3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Keywords - Ligandi

FAD, Flavoprotein

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-11759.
BRENDAi1.3.3.4. 3645.
UniPathwayiUPA00251; UER00324.

Names & Taxonomyi

Protein namesi
Recommended name:
Protoporphyrinogen oxidase, mitochondrial (EC:1.3.3.4)
Alternative name(s):
PX-2
Protoporphyrinogen IX oxidase isozyme II
Short name:
PPO II
Short name:
PPX II
Gene namesi
Name:PPXII
Synonyms:PPOX2
OrganismiNicotiana tabacum (Common tobacco)
Taxonomic identifieri4097 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeNicotianoideaeNicotianeaeNicotiana

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1926489.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001352731 – 504Protoporphyrinogen oxidase, mitochondrialAdd BLAST504

Expressioni

Developmental stagei

Expressed in expanding premature leaves. Decreased expression in oldest leaves. Also detected in roots.1 Publication

Inductioni

Oscillating expression during diurnal growth. Maximal expression in the dark period.1 Publication

Interactioni

Chemistry databases

BindingDBiO24164.

Structurei

Secondary structure

1504
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 19Combined sources5
Helixi23 – 33Combined sources11
Beta strandi38 – 42Combined sources5
Beta strandi44 – 48Combined sources5
Beta strandi54 – 57Combined sources4
Beta strandi60 – 65Combined sources6
Helixi74 – 82Combined sources9
Helixi86 – 88Combined sources3
Beta strandi98 – 108Combined sources11
Helixi113 – 118Combined sources6
Beta strandi119 – 122Combined sources4
Helixi124 – 131Combined sources8
Helixi133 – 136Combined sources4
Helixi152 – 160Combined sources9
Helixi162 – 166Combined sources5
Helixi169 – 177Combined sources9
Helixi181 – 183Combined sources3
Helixi186 – 189Combined sources4
Helixi191 – 199Combined sources9
Helixi203 – 210Combined sources8
Beta strandi236 – 238Combined sources3
Helixi243 – 250Combined sources8
Turni255 – 257Combined sources3
Beta strandi264 – 270Combined sources7
Beta strandi272 – 277Combined sources6
Beta strandi279 – 285Combined sources7
Beta strandi287 – 290Combined sources4
Beta strandi296 – 302Combined sources7
Helixi306 – 310Combined sources5
Beta strandi312 – 320Combined sources9
Beta strandi331 – 342Combined sources12
Helixi343 – 345Combined sources3
Beta strandi346 – 348Combined sources3
Beta strandi352 – 356Combined sources5
Helixi359 – 364Combined sources6
Beta strandi368 – 373Combined sources6
Helixi374 – 377Combined sources4
Helixi379 – 381Combined sources3
Beta strandi386 – 395Combined sources10
Helixi399 – 401Combined sources3
Helixi406 – 421Combined sources16
Beta strandi428 – 440Combined sources13
Helixi446 – 459Combined sources14
Beta strandi463 – 465Combined sources3
Beta strandi468 – 471Combined sources4
Helixi475 – 493Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SEZX-ray2.90A/B1-504[»]
ProteinModelPortaliO24164.
SMRiO24164.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO24164.

Family & Domainsi

Sequence similaritiesi

Belongs to the protoporphyrinogen oxidase family.Curated

Family and domain databases

Gene3Di3.50.50.60. 1 hit.
3.90.660.20. 1 hit.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_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.

O24164-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPSAGEDKH SSAKRVAVIG AGVSGLAAAY KLKIHGLNVT VFEAEGKAGG
60 70 80 90 100
KLRSVSQDGL IWDEGANTMT ESEGDVTFLI DSLGLREKQQ FPLSQNKRYI
110 120 130 140 150
ARNGTPVLLP SNPIDLIKSN FLSTGSKLQM LLEPILWKNK KLSQVSDSHE
160 170 180 190 200
SVSGFFQRHF GKEVVDYLID PFVAGTCGGD PDSLSMHHSF PELWNLEKRF
210 220 230 240 250
GSVILGAIRS KLSPKNEKKQ GPPKTSANKK RQRGSFSFLG GMQTLTDAIC
260 270 280 290 300
KDLREDELRL NSRVLELSCS CTEDSAIDSW SIISASPHKR QSEEESFDAV
310 320 330 340 350
IMTAPLCDVK SMKIAKRGNP FLLNFIPEVD YVPLSVVITT FKRENVKYPL
360 370 380 390 400
EGFGVLVPSK EQQHGLKTLG TLFSSMMFPD RAPNNVYLYT TFVGGSRNRE
410 420 430 440 450
LAKASRTELK EIVTSDLKQL LGAEGEPTYV NHLYWSKAFP LYGHNYDSVL
460 470 480 490 500
DAIDKMEKNL PGLFYAGNHR GGLSVGKALS SGCNAADLVI SYLESVSTDS

KRHC
Length:504
Mass (Da):55,407
Last modified:January 1, 1998 - v1
Checksum:iB85B55EC881DC00A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y13466 mRNA. Translation: CAA73866.1.
AB020500 mRNA. Translation: BAA34712.1.
AF044129 mRNA. Translation: AAD02291.1.
PIRiT04076.
RefSeqiNP_001312887.1. NM_001325958.1.
UniGeneiNta.3580.

Genome annotation databases

GeneIDi107815753.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y13466 mRNA. Translation: CAA73866.1.
AB020500 mRNA. Translation: BAA34712.1.
AF044129 mRNA. Translation: AAD02291.1.
PIRiT04076.
RefSeqiNP_001312887.1. NM_001325958.1.
UniGeneiNta.3580.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SEZX-ray2.90A/B1-504[»]
ProteinModelPortaliO24164.
SMRiO24164.
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

BindingDBiO24164.
ChEMBLiCHEMBL1926489.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi107815753.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00324.
BioCyciMetaCyc:MONOMER-11759.
BRENDAi1.3.3.4. 3645.

Miscellaneous databases

EvolutionaryTraceiO24164.

Family and domain databases

Gene3Di3.50.50.60. 1 hit.
3.90.660.20. 1 hit.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_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 nameiPPOM_TOBAC
AccessioniPrimary (citable) accession number: O24164
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.