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PDX3 pyridoxamine-phosphate oxidase PDX3 [ Saccharomyces cerevisiae S288C ]

Gene ID: 852323, updated on 6-Jul-2026
Official Symbol
PDX3
Official Full Name
pyridoxamine-phosphate oxidase PDX3
Primary source
SGD:S000000239
Locus tag
YBR035C
See related
AllianceGenome:SGD:S000000239; FungiDB:YBR035C; VEuPathDB:YBR035C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary
Enables FMN binding activity and pyridoxamine phosphate oxidase activity. Predicted to be involved in pyridoxal 5'-phosphate salvage. Predicted to act upstream of or within pyridoxine biosynthetic process. Located in mitochondrial intermembrane space. Human ortholog(s) of this gene implicated in pyridoxamine 5'-phosphate oxidase deficiency. Orthologous to human PNPO (pyridoxamine 5'-phosphate oxidase). [provided by Alliance of Genome Resources, Apr 2025]
Orthologs
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Location:
chromosome: II
Exon count:
1
Sequence:
Chromosome: II; NC_001134.8 (306269..306955, complement)

Chromosome II - NC_001134.8Genomic Context describing neighboring genes Neighboring gene Eds1p Neighboring gene protein-arginine omega-N methyltransferase HMT1 Neighboring gene ncRNA Neighboring gene ncRNA

Genomic Sequence:
NC_001134.8

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. Sterol uptake induced by an impairment of pyridoxal phosphate synthesis in Saccharomyces cerevisiae: cloning and sequencing of the PDX3 gene encoding pyridoxine (pyridoxamine) phosphate oxidase. Loubbardi A, et al. J Bacteriol, 1995 Apr. PMID 7896706, Free PMC Article
  2. The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene. Smits PH, et al. Yeast, 1994 Apr. PMID 8091864
  3. Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana. Sang Y, et al. FEBS Lett, 2007 Feb 6. PMID 17224143
  4. Pyridoxamine-phosphate oxidases and pyridoxamine-phosphate oxidase-related proteins catalyze the oxidation of 6-NAD(P)H to NAD(P). Marbaix AY, et al. Biochem J, 2019 Oct 30. PMID 31657440
  5. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Tanaka T, et al. Mol Biol Evol, 2005 Feb. PMID 15483325

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

Products Interactant Other Gene Complex Source Pubs Description

Homology

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables FMN binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables FMN binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity, acting on the CH-NH2 group of donors IEA
Inferred from Electronic Annotation
more info
  
enables pyridoxamine phosphate oxidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyridoxamine phosphate oxidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables pyridoxamine phosphate oxidase activity IEA
Inferred from Electronic Annotation
more info
  
enables pyridoxamine phosphate oxidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables pyridoxamine phosphate oxidase activity RCA
inferred from Reviewed Computational Analysis
more info
  
Process Evidence Code Pubs
involved_in pyridoxal 5'-phosphate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pyridoxal 5'-phosphate salvage IC
Inferred by Curator
more info
 PubMed 
involved_in pyridoxal 5'-phosphate salvage RCA
inferred from Reviewed Computational Analysis
more info
  
involved_in pyridoxine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in vitamin B6 metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol RCA
inferred from Reviewed Computational Analysis
more info
  
located_in mitochondrial intermembrane space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial intermembrane space IEA
Inferred from Electronic Annotation
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
Preferred Names
pyridoxamine-phosphate oxidase PDX3
NP_009591.1
  • Pyridoxine (pyridoxamine) phosphate oxidase; has homologs in E. coli and Myxococcus xanthus; transcription is under the general control of nitrogen metabolism

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_001134.8 Reference assembly

    Range
    306269..306955 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001178383.1 → NP_009591.1  pyridoxamine-phosphate oxidase PDX3

    See identical proteins and their annotated locations for NP_009591.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VQ35, P38075
    UniProtKB/TrEMBL
    B3LNB0
    Conserved Domains (1) summary
    COG0259
    Location:13 → 228
    PdxH; Pyridoxine/pyridoxamine 5'-phosphate oxidase [Coenzyme transport and metabolism]
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P38075.1

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