Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Protoporphyrinogen oxidase

Gene

hemY

Organism
Myxococcus xanthus
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

Catalytic activityi

Protoporphyrinogen-IX + 3 O2 = protoporphyrin-IX + 3 H2O2.1 Publication

Cofactori

FAD1 PublicationNote: Binds 1 FAD per subunit.1 Publication

Enzyme regulationi

Strongly inhibited by acifluorfen.1 Publication

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 sitei47FAD; via amide nitrogen1 Publication1
Binding sitei251FAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei408FADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi16 – 21FAD1 Publication6
Nucleotide bindingi39 – 40FAD1 Publication2
Nucleotide bindingi61 – 64FAD1 Publication4
Nucleotide bindingi446 – 448FAD1 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

BRENDAi1.3.3.4. 3551.
SABIO-RKP56601.
UniPathwayiUPA00251; UER00324.

Names & Taxonomyi

Protein namesi
Recommended name:
Protoporphyrinogen oxidase (EC:1.3.3.4)
Short name:
PPO
Gene namesi
Name:hemY
OrganismiMyxococcus xanthus
Taxonomic identifieri34 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaMyxococcalesCystobacterineaeMyxococcaceaeMyxococcus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001352671 – 471Protoporphyrinogen oxidaseAdd BLAST471

Interactioni

Subunit structurei

Monomer. Homodimer.2 Publications

Protein-protein interaction databases

STRINGi246197.MXAN_1293.

Structurei

Secondary structure

1471
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi12 – 15Combined sources4
Helixi19 – 29Combined sources11
Turni30 – 32Combined sources3
Beta strandi35 – 38Combined sources4
Beta strandi40 – 45Combined sources6
Beta strandi50 – 53Combined sources4
Beta strandi56 – 61Combined sources6
Helixi70 – 78Combined sources9
Helixi82 – 84Combined sources3
Beta strandi85 – 87Combined sources3
Beta strandi95 – 99Combined sources5
Beta strandi102 – 105Combined sources4
Helixi110 – 114Combined sources5
Beta strandi117 – 119Combined sources3
Helixi121 – 128Combined sources8
Helixi129 – 132Combined sources4
Helixi144 – 151Combined sources8
Helixi154 – 159Combined sources6
Helixi161 – 169Combined sources9
Turni173 – 175Combined sources3
Helixi178 – 181Combined sources4
Helixi183 – 192Combined sources10
Helixi195 – 206Combined sources12
Beta strandi223 – 226Combined sources4
Helixi231 – 241Combined sources11
Helixi242 – 244Combined sources3
Beta strandi245 – 255Combined sources11
Beta strandi262 – 267Combined sources6
Beta strandi270 – 275Combined sources6
Beta strandi277 – 281Combined sources5
Helixi285 – 292Combined sources8
Turni293 – 295Combined sources3
Helixi297 – 304Combined sources8
Beta strandi311 – 318Combined sources8
Beta strandi328 – 332Combined sources5
Helixi335 – 337Combined sources3
Beta strandi343 – 346Combined sources4
Helixi347 – 350Combined sources4
Helixi352 – 354Combined sources3
Beta strandi360 – 367Combined sources8
Helixi372 – 376Combined sources5
Helixi379 – 394Combined sources16
Beta strandi401 – 410Combined sources10
Helixi419 – 431Combined sources13
Beta strandi436 – 438Combined sources3
Turni441 – 443Combined sources3
Helixi448 – 462Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IVDX-ray2.30A/B4-471[»]
2IVEX-ray2.70A/B4-471[»]
ProteinModelPortaliP56601.
SMRiP56601.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56601.

Family & Domainsi

Sequence similaritiesi

Belongs to the protoporphyrinogen oxidase family.Curated

Phylogenomic databases

eggNOGiENOG4105C1Q. Bacteria.
COG1232. LUCA.

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.

P56601-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHHMPRTTGM NVAVVGGGIS GLAVAHHLRS RGTDAVLLES SARLGGAVGT
60 70 80 90 100
HALAGYLVEQ GPNSFLDREP ATRALAAALN LEGRIRAADP AAKRRYVYTR
110 120 130 140 150
GRLRSVPASP PAFLASDILP LGARLRVAGE LFSRRAPEGV DESLAAFGRR
160 170 180 190 200
HLGHRATQVL LDAVQTGIYA GDVEQLSVAA TFPMLVKMER EHRSLILGAI
210 220 230 240 250
RAQKAQRQAA LPAGTAPKLS GALSTFDGGL QVLIDALAAS LGDAAHVGAR
260 270 280 290 300
VEGLAREDGG WRLIIEEHGR RAELSVAQVV LAAPAHATAK LLRPLDDALA
310 320 330 340 350
ALVAGIAYAP IAVVHLGFDA GTLPAPDGFG FLVPAEEQRR MLGAIHASTT
360 370 380 390 400
FPFRAEGGRV LYSCMVGGAR QPGLVEQDED ALAALAREEL KALAGVTARP
410 420 430 440 450
SFTRVFRWPL GIPQYNLGHL ERVAAIDAAL QRLPGLHLIG NAYKGVGLND
460 470
CIRNAAQLAD ALVAGNTSHA P
Length:471
Mass (Da):49,388
Last modified:December 15, 1998 - v1
Checksum:i2E9909D464F81515
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27429 Genomic DNA. Translation: AAM28643.1.
AF098938 Genomic DNA. Translation: AAD13609.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27429 Genomic DNA. Translation: AAM28643.1.
AF098938 Genomic DNA. Translation: AAD13609.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IVDX-ray2.30A/B4-471[»]
2IVEX-ray2.70A/B4-471[»]
ProteinModelPortaliP56601.
SMRiP56601.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246197.MXAN_1293.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C1Q. Bacteria.
COG1232. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00324.
BRENDAi1.3.3.4. 3551.
SABIO-RKP56601.

Miscellaneous databases

EvolutionaryTraceiP56601.

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_MYXXA
AccessioniPrimary (citable) accession number: P56601
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: December 15, 1998
Last modified: November 2, 2016
This is version 96 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

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.