PNPO pyridoxamine 5'-phosphate oxidase [Homo sapiens (human)] - Gene

Summary

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Official Symbol: PNPOprovided by HGNC
Official Full Name: pyridoxamine 5'-phosphate oxidaseprovided by HGNC
Primary source: HGNC:30260
See related: HPRD:04476; MIM:603287
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDXPO
Summary: The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]

Genomic context

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Location :: 17q21.32

Sequence :: Chromosome: 17; NC_000017.10 (46018889..46026674)

See PNPO in Epigenomics, MapViewer

Chromosome 17 - NC_000017.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

provide evidence that a single arginine residue of the C terminus of pyridoxal 5'-phosphate synthase is responsible for coordinating co-operativity in this elaborate protein machinery
Title: It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase.
PNP oxidase R229W mutation identified in patients with neonatal epileptic encephalopathy sgnificantly affect the catalytic efficiency of the enzyme.
Title: Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder.
Sequencing of the PNPO gene revealed a novel homozygous nonsense mutationt in exon 3 in the neonatal and infantile seizure.
Title: PNPO deficiency: an under diagnosed inborn error of pyridoxine metabolism.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association between PNPO and schizophrenia in the Japanese population.
We examined 8 single nucleotide polymorphisms (SNPs) in PNPO and its 5'-flanking regions in 359 schizophrenia patients and 582 control subjects.
Title: Association between PNPO and schizophrenia in the Japanese population.
several mutations appear to cause epilepsy
Title: Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5'-phosphate oxidase.
Results describe a combined computer and biochemical approach to characterize human pyridoxine 5'-phosphate oxidase (PNPO).
Title: Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Pyridoxal 5'-phosphate-dependent epilepsy

MIM: 610090

Genetic Testing Registry

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
BioGRID:120463	BioGRID:106848	APP	BioGRID	PubMed	Reconstituted Complex
BioGRID:120463	BioGRID:108309	ELAVL1	BioGRID	PubMed	Affinity Capture-RNA
BioGRID:120463	BioGRID:110208	LPP	BioGRID	PubMed	Co-fractionation
BioGRID:120463	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

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Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only ...
Metabolism of water-soluble vitamins and cofactors, organism-specific biosystem (from REACTOME)
Metabolism of water-soluble vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only ...
Selenium Pathway, organism-specific biosystem (from WikiPathways)
Selenium Pathway, organism-specific biosystem
Selenium Pathway
Vitamin B6 metabolism, organism-specific biosystem (from KEGG)
Vitamin B6 metabolism, organism-specific biosystem
Vitamin B6 metabolism
Vitamin B6 metabolism, conserved biosystem (from KEGG)
Vitamin B6 metabolism, conserved biosystem
Vitamin B6 metabolism
Vitamins B6 activation to pyridoxal phosphate, organism-specific biosystem (from REACTOME)
Vitamins B6 activation to pyridoxal phosphate, organism-specific biosystemAnimals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally...
pyridoxal 5'-phosphate salvage pathway, organism-specific biosystem (from BIOCYC)
pyridoxal 5'-phosphate salvage pathway, organism-specific biosystem
pyridoxal 5'-phosphate salvage pathway

General gene information

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Markers

D17S2044 (e-PCR)
- UniSTS:15373

D17S1785 (e-PCR), detects polymorphism
- UniSTS:43042

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

STS-AA005137 (e-PCR)
- UniSTS:32348

STS-AA005137 (e-PCR)
- UniSTS:53089

D1S1423 (e-PCR)
- UniSTS:149619

Genotypes

See PNPO SNP Geneview Report
See PNPO SNP Genotype Report
See PNPO SNP Variation Viewer Report

Homology

Homologs of the PNPO gene: The PNPO gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, and N.crassa.
Map Viewer (Mouse)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
FMN binding	IEA Inferred from Electronic Annotation more info
pyridoxamine-phosphate oxidase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
pyridoxine biosynthetic process	IEA Inferred from Electronic Annotation more info
small molecule metabolic process	TAS Traceable Author Statement more info
vitamin B6 metabolic process	TAS Traceable Author Statement more info
vitamin metabolic process	TAS Traceable Author Statement more info
water-soluble vitamin metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: pyridoxine-5'-phosphate oxidase

Names: pyridoxine-5'-phosphate oxidase; pyridoxamine-phosphate oxidase; pyridoxal 5'-phosphate synthase; pyridoxine 5'-phosphate oxidase

NP_060599.1

EC 1.4.3.5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008744.1 RefSeqGene

Range

5001..12786

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_018129.3 → NP_060599.1 pyridoxine-5'-phosphate oxidase

Status: REVIEWED

Source sequence(s)

AC018521, AK001397, BC006525, CB853441, DB228906

Consensus CDS

CCDS11522.1

UniProtKB/Swiss-Prot

Q9NVS9

Conserved Domains (3) summary

pfam01243
Location:75 – 153
Blast Score: 236

Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase

pfam10590
Location:206 – 261
Blast Score: 161

PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region

TIGR00558
Location:57 – 261
Blast Score: 769

pdxH; pyridoxamine-phosphate oxidase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000017.10 Reference GRCh37.p10 Primary Assembly

Range

46018889..46026674

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000149.1 Alternate HuRef

Range

41387555..41395352

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018928.1 Alternate CHM1_1.0

Range

47033684..47041470

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01041150.1 (3679..11476)	None
genomic	AC018521.8 (48428..55648)	None
genomic	AMYH01008451.1 (232492..240278)	None
genomic	CH471109.2	EAW94770.1
		EAW94771.1
mRNA	AF468030.1	AAM76918.1
mRNA	AK001397.1	BAA91668.1
mRNA	AK223242.1	BAD96962.1
mRNA	AK303536.1	BAG64562.1
mRNA	AK303665.1	BAG64664.1
mRNA	AK303792.1	BAG64749.1
mRNA	BC006525.2	AAH06525.1
mRNA	CB853441.1	None
mRNA	DA186382.1	None
mRNA	DB228906.1	None

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
Q9NVS9.1	GenPept	UniProtKB/Swiss-Prot:Q9NVS9

Additional links

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Additional Links

Epigenomics
MIM 603287
BIOMDB: Database of Mutations Causing Tetrahyrdobiopterin Deficiencies www.biopku.org/dbsearches/BIOMDB_Start.asp
PNPO homepage - Mendelian genes PNPO
UCSC UCSC
UniGene Hs.631742