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Protein

Pyridoxamine 5'-phosphate oxidase

Gene

PDX3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.

Cofactori

FMNNote: Binds 1 FMN per subunit.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxamine 5'-phosphate oxidase (PDX3)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxamine 5'-phosphate oxidase (PDX3)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei78Pyridoxal 5'-phosphateBy similarity1
Binding sitei118FMNBy similarity1
Binding sitei136Pyridoxal 5'-phosphateBy similarity1
Binding sitei140Pyridoxal 5'-phosphateBy similarity1
Binding sitei144Pyridoxal 5'-phosphateBy similarity1
Binding sitei199FMNBy similarity1
Binding sitei209FMNBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi73 – 76FMN1 Publication4
Nucleotide bindingi88 – 89FMN1 Publication2
Nucleotide bindingi95 – 96FMN1 Publication2
Nucleotide bindingi153 – 154FMN1 Publication2

GO - Molecular functioni

  • FMN binding Source: SGD
  • pyridoxamine-phosphate oxidase activity Source: SGD

GO - Biological processi

  • pyridoxal 5'-phosphate salvage Source: SGD
  • pyridoxine biosynthetic process Source: UniProtKB-KW

Keywordsi

Molecular functionOxidoreductase
Biological processPyridoxine biosynthesis
LigandFlavoprotein, FMN

Enzyme and pathway databases

BioCyciMetaCyc:YBR035C-MONOMER
YEAST:YBR035C-MONOMER
ReactomeiR-SCE-964975 Vitamins B6 activation to pyridoxal phosphate
UniPathwayiUPA01068; UER00304
UPA01068; UER00305

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Gene namesi
Name:PDX3
Ordered Locus Names:YBR035C
ORF Names:YBR0321
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR035C
SGDiS000000239 PDX3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001677871 – 228Pyridoxamine 5'-phosphate oxidaseAdd BLAST228

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP38075
PaxDbiP38075
PRIDEiP38075

PTM databases

iPTMnetiP38075

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi32736, 260 interactors
DIPiDIP-4324N
IntActiP38075, 4 interactors
STRINGi4932.YBR035C

Structurei

Secondary structure

1228
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi28 – 30Combined sources3
Helixi35 – 48Combined sources14
Beta strandi57 – 64Combined sources8
Turni65 – 68Combined sources4
Beta strandi69 – 76Combined sources8
Beta strandi82 – 90Combined sources9
Beta strandi92 – 94Combined sources3
Helixi95 – 102Combined sources8
Beta strandi105 – 112Combined sources8
Turni113 – 116Combined sources4
Beta strandi117 – 127Combined sources11
Helixi130 – 139Combined sources10
Helixi142 – 150Combined sources9
Beta strandi156 – 158Combined sources3
Helixi160 – 173Combined sources14
Beta strandi186 – 200Combined sources15
Beta strandi208 – 213Combined sources6
Beta strandi222 – 226Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1CI0X-ray2.70A/B1-228[»]
ProteinModelPortaliP38075
SMRiP38075
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38075

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni20 – 23Pyridoxal 5'-phosphate bindingBy similarity4
Regioni205 – 207Pyridoxal 5'-phosphate bindingBy similarity3

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000011219
HOGENOMiHOG000242755
KOiK00275
OMAiPEPNAMV
OrthoDBiEOG092C54QW

Family and domain databases

Gene3Di2.30.110.10, 1 hit
HAMAPiMF_01629 PdxH, 1 hit
InterProiView protein in InterPro
IPR000659 Pyridox_Oxase
IPR019740 Pyridox_Oxase_CS
IPR011576 Pyridox_Oxase_put
IPR019576 Pyridoxamine_oxidase_dimer_C
IPR012349 Split_barrel_FMN-bd
PANTHERiPTHR10851:SF0 PTHR10851:SF0, 1 hit
PfamiView protein in Pfam
PF10590 PNP_phzG_C, 1 hit
PF01243 Putative_PNPOx, 1 hit
PIRSFiPIRSF000190 Pyd_amn-ph_oxd, 1 hit
TIGRFAMsiTIGR00558 pdxH, 1 hit
PROSITEiView protein in PROSITE
PS01064 PYRIDOX_OXIDASE, 1 hit

Sequencei

Sequence statusi: Complete.

P38075-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP
60 70 80 90 100
RETLPEAITF SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI
110 120 130 140 150
ATNPNAAIVF FWKDLQRQVR VEGITEHVNR ETSERYFKTR PRGSKIGAWA
160 170 180 190 200
SRQSDVIKNR EELDELTQKN TERFKDAEDI PCPDYWGGLR IVPLEIEFWQ
210 220
GRPSRLHDRF VYRRKTENDP WKVVRLAP
Length:228
Mass (Da):26,908
Last modified:October 1, 1994 - v1
Checksum:i8B648A219763160E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76078 Genomic DNA Translation: CAA53690.1
X76992 Genomic DNA Translation: CAA54295.1
Z35904 Genomic DNA Translation: CAA84977.1
AY557712 Genomic DNA Translation: AAS56038.1
BK006936 Genomic DNA Translation: DAA07155.1
PIRiS41301
RefSeqiNP_009591.1, NM_001178383.1

Genome annotation databases

EnsemblFungiiYBR035C; YBR035C; YBR035C
GeneIDi852323
KEGGisce:YBR035C

Similar proteinsi

Entry informationi

Entry nameiPDX3_YEAST
AccessioniPrimary (citable) accession number: P38075
Secondary accession number(s): D6VQ35
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: March 28, 2018
This is version 165 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health