protein coding gene - pdx3 (SPAC1093.02) - pyridoxamine 5'-phosphate oxidase Pdx3

Gene summary

Standard name: pdx3
Systematic ID: SPAC1093.02
Product: pyridoxamine 5'-phosphate oxidase Pdx3
Organism: Schizosaccharomyces pombe (fission yeast)
UniProt ID: Q9UTQ1
ORFeome ID: 08/08B05
Characterisation status: biological role inferred
Feature type: mRNA gene
Genomic location: chromosome I: 4612115..4613297 forward strand

Annotation

Disease association

MONDO:0012407 - pyridoxal phosphate-responsive seizures

References:

PB_REF:0000006

GO biological process

GO:0042823 - pyridoxal 5'-phosphate biosynthetic process

References:

GO_REF:0000033

GO:0042818 - pyridoxamine metabolic process

References:

GO_REF:0000111

GO:0008615 - pyridoxine biosynthetic process

References:

GO_REF:0000002

GO cellular component

GO:0005739 - mitochondrion

References:

GO_REF:0000033

GO molecular function

GO:0010181 - FMN binding

References:

GO_REF:0000002

GO:0004733 - pyridoxamine phosphate oxidase activity

References:

GO_REF:0000033

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00047 - O-phospho-L-threonine

References:

MOD:00048 - O4'-phospho-L-tyrosine

References:

PMID:33823663

MOD:01148 - ubiquitinylated lysine

References:

PMID:37970674

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000011 - RNA level increased

References:

PMID:33313903

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

PMID:23101633

Single locus phenotype

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

pdx3delta

FYPO:0002177 - viable vegetative cell with normal cell morphology

References:

PMID:23697806

Genotypes:

pdx3delta

Taxonomic conservation

PBO:0011067 - conserved in bacteria

PBO:0011065 - conserved in eukaryotes

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

ID	Name	InterPro name	DB name
PF10590	PNP_phzG_C	Pyridoxamine_oxidase_dimer_C	PFAM
PF01243	PNPOx_N	Pyridox_Oxase_N	PFAM
PS01064	PYRIDOX_OXIDASE	Pyridox_Oxase_CS	PROSITE_PATTERNS
G3DSA:2.30.110.10:FF:000010			FUNFAM
SSF50475	FMN-binding split barrel		SUPERFAMILY
G3DSA:2.30.110.10		Split_barrel_FMN-bd	GENE3D
PTHR10851	PYRIDOXINE-5-PHOSPHATE OXIDASE	Pyridox_Oxase	PANTHER
PIRSF000190	Pyd_amn-ph_oxd	Pyridox_Oxase	PIRSF
Coil	Coil		COILS
MF_01629	PdxH	Pyridox_Oxase	HAMAP
TIGR00558	pdxH	Pyridox_Oxase	NCBIFAM
NF004231	PRK05679.1		NCBIFAM

Orthologs

PNPO (HGNC:30260) Homo sapiens
pdx3 (SJAG_01881) Schizosaccharomyces japonicus
PDX3 (YBR035C) Saccharomyces cerevisiae

References / Literature

PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.: Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:39705284 - Proteomic and phosphoproteomic analyses reveal that TORC1 is reactivated by pheromone signaling during sexual reproduction in fission yeast.: Bérard M et al. PLoS Biol 2024 Dec 20;22(12):e3002963
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.: Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.: Halova L et al. Open Biol 2021 Apr;11(4):200405
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).: Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.: Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.: Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:21511999 - Comparative functional genomics of the fission yeasts.: Rhind N et al. Science 2011 May 20;332(6032):930-6
GO_REF:0000002 - Comments
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.: Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.: Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.: Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:25375137 - Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability.: Hasan A et al. PLoS Genet 2014 Nov;10(11):e1004684
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.: Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference