Human Gene PNPO (uc002imo.3) Description and Page Index
  Description: Homo sapiens pyridoxamine 5'-phosphate oxidase (PNPO), mRNA.
RefSeq Summary (NM_018129): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK001397.1, SRR7346977.1085016.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:46,018,889-46,026,674 Size: 7,786 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr17:46,019,042-46,024,148 Size: 5,107 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr17:46,018,889-46,026,674)mRNA (may differ from genome)Protein (261 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Pyridoxine-5'-phosphate oxidase; EC=; AltName: Full=Pyridoxamine-phosphate oxidase;
FUNCTION: Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
CATALYTIC ACTIVITY: Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2).
CATALYTIC ACTIVITY: Pyridoxine 5'-phosphate + O(2) = pyridoxal 5'- phosphate + H(2)O(2).
COFACTOR: Binds 1 FMN per subunit.
PATHWAY: Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1.
PATHWAY: Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
SUBUNIT: Homodimer.
DISEASE: Defects in PNPO are the cause of pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:610090]; also known as PNPO-related neonatal epileptic encephalopathy. The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine.
SIMILARITY: Belongs to the pyridoxamine 5'-phosphate oxidase family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PNPO
CDC HuGE Published Literature: PNPO

-  MalaCards Disease Associations
  MalaCards Gene Search: PNPO
Diseases sorted by gene-association score: pyridoxamine 5'-phosphate oxidase deficiency* (1550), pyridoxal 5'-phosphate-dependent epilepsy* (500), seizure disorder* (241), visual epilepsy* (121), encephalopathy (11), hypophosphatasia, infantile (8), benign familial infantile epilepsy (5), epileptic encephalopathy, early infantile, 15 (4), epileptic encephalopathy, early infantile, 6 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.68 RPKM in Liver
Total median expression: 348.48 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.40153-0.382 Picture PostScript Text
3' UTR -872.442526-0.345 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000659 - Pyridox_Oxase
IPR019740 - Pyridox_Oxase_CS
IPR011576 - Pyridox_Oxase_FMN-bd
IPR019576 - Pyridoxamine_oxidase_dimer_C
IPR012349 - Split_barrel_FMN-bd
IPR009002 - Split_barrel_FMN-bd-related

Pfam Domains:
PF01243 - Pyridoxamine 5'-phosphate oxidase
PF10590 - Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region
PF12766 - Pyridoxamine 5'-phosphate oxidase

SCOP Domains:
50475 - FMN-binding split barrel

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9NVS9
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004733 pyridoxamine-phosphate oxidase activity
GO:0005515 protein binding
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
GO:0048037 cofactor binding

Biological Process:
GO:0008615 pyridoxine biosynthetic process
GO:0042816 vitamin B6 metabolic process
GO:0042823 pyridoxal phosphate biosynthetic process
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005654 nucleoplasm
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  LF209297 - JP 2014500723-A/16800: Polycomb-Associated Non-Coding RNAs.
AK303792 - Homo sapiens cDNA FLJ59601 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC
AK303665 - Homo sapiens cDNA FLJ59599 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC
AK001397 - Homo sapiens cDNA FLJ10535 fis, clone NT2RP2001070, weakly similar to PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (EC
JD554813 - Sequence 535837 from Patent EP1572962.
AK223242 - Homo sapiens mRNA for pyridoxine 5'-phosphate oxidase variant, clone: STM03705.
AK303536 - Homo sapiens cDNA FLJ59109 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC
BC006525 - Homo sapiens pyridoxamine 5'-phosphate oxidase, mRNA (cDNA clone MGC:953 IMAGE:2966366), complete cds.
GQ900985 - Homo sapiens clone HEL-T-97 epididymis secretory sperm binding protein mRNA, complete cds.
JD408363 - Sequence 389387 from Patent EP1572962.
KJ899086 - Synthetic construct Homo sapiens clone ccsbBroadEn_08480 PNPO gene, encodes complete protein.
KR709978 - Synthetic construct Homo sapiens clone CCSBHm_00008609 PNPO (PNPO) mRNA, encodes complete protein.
KR709979 - Synthetic construct Homo sapiens clone CCSBHm_00008610 PNPO (PNPO) mRNA, encodes complete protein.
KR709980 - Synthetic construct Homo sapiens clone CCSBHm_00008612 PNPO (PNPO) mRNA, encodes complete protein.
KR712208 - Synthetic construct Homo sapiens clone CCSBHm_00900160 PNPO (PNPO) mRNA, encodes complete protein.
AF468030 - Homo sapiens pyridoxine-5'-phosphate oxidase mRNA, complete cds.
FJ224333 - Homo sapiens epididymis secretory protein Li 302 (HEL-S-302) mRNA, complete cds.
LF327505 - JP 2014500723-A/135008: Polycomb-Associated Non-Coding RNAs.
JD511664 - Sequence 492688 from Patent EP1572962.
JD153836 - Sequence 134860 from Patent EP1572962.
JD259686 - Sequence 240710 from Patent EP1572962.
JD152884 - Sequence 133908 from Patent EP1572962.
JD038724 - Sequence 19748 from Patent EP1572962.
JD422823 - Sequence 403847 from Patent EP1572962.
JD521517 - Sequence 502541 from Patent EP1572962.
JD071922 - Sequence 52946 from Patent EP1572962.
JD411274 - Sequence 392298 from Patent EP1572962.
JD285402 - Sequence 266426 from Patent EP1572962.
JD373646 - Sequence 354670 from Patent EP1572962.
JD455299 - Sequence 436323 from Patent EP1572962.
JD184143 - Sequence 165167 from Patent EP1572962.
JD505236 - Sequence 486260 from Patent EP1572962.
JD117383 - Sequence 98407 from Patent EP1572962.
JD138054 - Sequence 119078 from Patent EP1572962.
JD441771 - Sequence 422795 from Patent EP1572962.
JD329861 - Sequence 310885 from Patent EP1572962.
JD103138 - Sequence 84162 from Patent EP1572962.
JD130473 - Sequence 111497 from Patent EP1572962.
JD049745 - Sequence 30769 from Patent EP1572962.
JD470451 - Sequence 451475 from Patent EP1572962.
JD363061 - Sequence 344085 from Patent EP1572962.
JD340609 - Sequence 321633 from Patent EP1572962.
JD202811 - Sequence 183835 from Patent EP1572962.
JD244058 - Sequence 225082 from Patent EP1572962.
JD053376 - Sequence 34400 from Patent EP1572962.
AB209036 - Homo sapiens mRNA for proteasome 26S ATPase subunit 5 variant protein.
MA563082 - JP 2018138019-A/135008: Polycomb-Associated Non-Coding RNAs.
MA444874 - JP 2018138019-A/16800: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00750 - Vitamin B6 metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PLPSAL-PWY - pyridoxal 5'-phosphate salvage pathway

Reactome (by CSHL, EBI, and GO)

Protein Q9NVS9 (Reactome details) participates in the following event(s):

R-HSA-965019 2xPNPO:2xFMN oxidizes PDXP to PXLP
R-HSA-965079 2xPNPO:2xFMN oxidizes PXAP to PXLP
R-HSA-964975 Vitamins B6 activation to pyridoxal phosphate
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: D3DTT9, NM_018129, NP_060599, PNPO_HUMAN, Q9NVS9
UCSC ID: uc002imo.3
RefSeq Accession: NM_018129
Protein: Q9NVS9 (aka PNPO_HUMAN)
CCDS: CCDS11522.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_018129.3
exon count: 7CDS single in 3' UTR: no RNA size: 3482
ORF size: 786CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1672.00frame shift in genome: no % Coverage: 99.51
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.