Tchem PNPO Pyridoxine-5'-phosphate oxidase

Protein Summary

Description

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

Uniprot Accession IDs

• Q9NVS9
• B4E0V0
• B4E152
• B4E1D7
• D3DTT9

Gene Name

• PNPO

Ensembl ID

• ENST00000225573
• ENSP00000225573
• ENSG00000108439
• ENST00000434554
• ENSP00000399960
• ENST00000582171
• ENSP00000463994
• ENST00000585320
• ENSP00000462345
• ENST00000641856
• ENSP00000493224
• ENST00000642017
• ENSP00000493302

Symbol

• PDXPO
• HEL-S-302

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
kinase perturbation	0.88
transcription factor perturbation	0.84
histone modification site profile	0.8
disease perturbation	0.79
virus perturbation	0.79

Protein Classes

PANTHER Classes

Protein / Oxidoreductase / Oxidase / Pyridoxine-5'-phosphate Oxidase

DTO Classes

Protein / Enzyme / Oxidoreductase / Oxidase / Pyridoxine-5'-phosphate Oxidase

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 113.4   (req: < 5)

Gene RIFs: 13   (req: <= 3)

Antibodies: 322   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 113.4   (req: >= 5)

Gene RIFs: 13   (req: > 3)

Antibodies: 322   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 7

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 1

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

Find Targets by Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (1)

Explore Active Ligands

1 – 1 of 1

(4-ethynyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate

PNPOTchem Enzyme

pKi : 6.26

Protein-Protein Interactions (75)

Explore Interacting Targets

1 – 10 of 75

• See Interactions on String-DB

MTERF1

Tbio

Novelty:  0.00983613

p_int:  0.999999998

p_ni:  2e-9

Score:  0.485

Data Source:  BioPlex,STRINGDB

SPANXN4

Tdark

Novelty:  1.91062423

p_int:  0.999877878

p_ni:  0.000122122

Data Source:  BioPlex

MOK

Tbio

Family:  Kinase

Novelty:  0.0116106

p_int:  0.999247511

p_ni:  0.000537138

p_wrong:  0.00021535

Score:  0.534

Data Source:  BioPlex,STRINGDB

FBXO25

Tbio

Novelty:  0.1205608

p_int:  0.989270973

p_ni:  0.005529442

p_wrong:  0.005199584

Score:  0.534

Data Source:  BioPlex,STRINGDB

ARL6IP6

Tdark

Novelty:  0.36643453

p_int:  0.988615387

p_ni:  0.007537365

p_wrong:  0.003847247

Score:  0.2

Data Source:  BioPlex,STRINGDB

CARTPT

Tbio

Novelty:  0.00224864

p_int:  0.931878281

p_ni:  0.056639261

p_wrong:  0.011482458

Data Source:  BioPlex

SLC25A32

Tbio

Family:  Transporter

Novelty:  0.06270404

p_int:  0.930177477

p_ni:  0.069818556

p_wrong:  0.000003966

Score:  0.267

Data Source:  BioPlex,STRINGDB

FGB

Tbio

Novelty:  0.00437751

p_int:  0.920965506

p_ni:  0.078973821

p_wrong:  0.000060672

Data Source:  BioPlex

PDXK

Tbio

Family:  Kinase

Novelty:  0.00976418

Score:  0.99

Data Source:  STRINGDB

PHOSPHO2

Tdark

Family:  Enzyme

Novelty:  0.36911271

Score:  0.952

Data Source:  STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (15)

Reactome (4)

KEGG (2)

PathwayCommons (5)

UniProt (2)

WikiPathways (2)

Metabolism (R-HSA-1430728)

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1 – 4 of 4

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Metabolism	2112 targets	R-HSA-1430728
Reactome	Metabolism of vitamins and cofactors	188 targets	R-HSA-196854
Reactome	Metabolism of water-soluble vitamins and cofactors	122 targets	R-HSA-196849
Reactome	Vitamins B6 activation to pyridoxal phosphate	3 targets	R-HSA-964975

Name	Explore in Pharos	Explore in Source
Metabolism	2112 targets	R-HSA-1430728
Metabolism of vitamins and cofactors	188 targets	R-HSA-196854
Metabolism of water-soluble vitamins and cofactors	122 targets	R-HSA-196849
Vitamins B6 activation to pyridoxal phosphate	3 targets	R-HSA-964975

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (9)

Functions (4)

Components (2)

Processes (3)

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1 – 4 of 4

GO Term	Evidence	Assigned by
FMN binding	Inferred from Direct Assay (IDA)	CAFA
protein homodimerization activity	Inferred from Direct Assay (IDA)	CAFA
pyridoxal phosphate binding	Inferred from Direct Assay (IDA)	CAFA
pyridoxamine-phosphate oxidase activity	Inferred from Direct Assay (IDA)	CAFA

Disease Associations (null)

No disease associations found

GWAS Traits (15)

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1 – 5 of 15

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
hair color	EFO_0003924	2	3	0	1.1	93.5
BMI-adjusted hip circumference	EFO_0008039	2	4	5		77.3
hematocrit	EFO_0004348	1	1	1		63.4
neutrophil count	EFO_0004833	2	2	2		46.9
type II diabetes mellitus	EFO_0001360	1	1	1		40.7

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
hair color	EFO_0003924	0	1.1	93.5
BMI-adjusted hip circumference	EFO_0008039	5		77.3
hematocrit	EFO_0004348	1		63.4
neutrophil count	EFO_0004833	2		46.9
type II diabetes mellitus	EFO_0001360	1		40.7

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UniProt Keyword Find Similar Targets

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3D-structure
Alternative splicing
Complete proteome
Direct protein sequencing
Disease mutation
Epilepsy
Flavoprotein
FMN
Oxidoreductase
Phosphoprotein

GWAS Trait Find Similar Targets

No Header	No Header
birth weight
BMI-adjusted hip circumference
body height
epilepsy
generalised epilepsy
hair color
hair colour measurement
heel bone mineral density
hematocrit
high density lipoprotein cholesterol measurement

IDG Resources

No IDG generated resources found

Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	pyridoxamine 5'-phosphate oxidase	VGNC:9532	749248
Macaque	pyridoxamine 5'-phosphate oxidase		694949
Mouse	pyridoxine 5'-phosphate oxidase	MGI:2144151	103711
Rat	pyridoxamine 5'-phosphate oxidase	RGD:621456	64533
Dog	pyridoxamine 5'-phosphate oxidase	VGNC:44759	480540

Species	Name	OMA	EggNOG	Inparanoid
Chimp	pyridoxamine 5'-phosphate oxidase
Macaque	pyridoxamine 5'-phosphate oxidase
Mouse	pyridoxine 5'-phosphate oxidase
Rat	pyridoxamine 5'-phosphate oxidase
Dog	pyridoxamine 5'-phosphate oxidase

Publication Statistics

PubMed Score 113.40

PubMed score by year

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PubTator Score 61.32

PubTator score by year

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Related Publications

Text Mined References (25)

GeneRif Annotations (13)

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10

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PMID	Year	Title