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Protein

Pyridoxine-5'-phosphate oxidase

Gene

PNPO

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).1 Publication

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.

Cofactori

FMN1 PublicationNote: Binds 1 FMN per subunit.1 Publication

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine-5'-phosphate oxidase (PNPO)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine-5'-phosphate oxidase (PNPO)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei100Pyridoxal 5'-phosphate1 Publication1
Binding sitei139FMNBy similarity1
Binding sitei157Pyridoxal 5'-phosphate1 Publication1
Binding sitei161Pyridoxal 5'-phosphate1 Publication1
Binding sitei165Pyridoxal 5'-phosphate1 Publication1
Binding sitei219FMNBy similarity1
Binding sitei229FMNBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi95 – 98FMN1 Publication4
Nucleotide bindingi110 – 111FMN1 Publication2
Nucleotide bindingi116 – 117FMN1 Publication2
Nucleotide bindingi174 – 175FMN1 Publication2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS03105-MONOMER.
ZFISH:HS03105-MONOMER.
ReactomeiR-HSA-964975. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RKQ9NVS9.
UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine-5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
Pyridoxamine-phosphate oxidase
Gene namesi
Name:PNPO
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:30260. PNPO.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytosol Source: Reactome
  • extracellular exosome Source: UniProtKB
  • nucleoplasm Source: HPA
Complete GO annotation...

Pathology & Biotechi

Involvement in diseasei

Pyridoxine-5'-phosphate oxidase deficiency (PNPOD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionThe 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,.
See also OMIM:610090
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_029360229R → W in PNPOD; strong activity decrease. 1 PublicationCorresponds to variant rs104894629dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi55163.
MalaCardsiPNPO.
MIMi610090. phenotype.
OpenTargetsiENSG00000108439.
Orphaneti79096. Pyridoxal phosphate-responsive seizures.
PharmGKBiPA134915565.

Chemistry databases

ChEMBLiCHEMBL3271932.

Polymorphism and mutation databases

BioMutaiPNPO.
DMDMi37082126.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001677831 – 261Pyridoxine-5'-phosphate oxidaseAdd BLAST261

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei238PhosphothreonineCombined sources1
Modified residuei241PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9NVS9.
PaxDbiQ9NVS9.
PeptideAtlasiQ9NVS9.
PRIDEiQ9NVS9.

2D gel databases

REPRODUCTION-2DPAGEIPI00018272.

PTM databases

iPTMnetiQ9NVS9.
PhosphoSitePlusiQ9NVS9.

Expressioni

Gene expression databases

BgeeiENSG00000108439.
CleanExiHS_PNPO.
ExpressionAtlasiQ9NVS9. baseline and differential.
GenevisibleiQ9NVS9. HS.

Organism-specific databases

HPAiHPA023204.
HPA027776.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi120463. 23 interactors.
IntActiQ9NVS9. 2 interactors.
STRINGi9606.ENSP00000225573.

Chemistry databases

BindingDBiQ9NVS9.

Structurei

Secondary structure

1261
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi58 – 71Combined sources14
Beta strandi80 – 86Combined sources7
Beta strandi88 – 90Combined sources3
Beta strandi92 – 98Combined sources7
Beta strandi102 – 105Combined sources4
Beta strandi106 – 112Combined sources7
Helixi116 – 123Combined sources8
Beta strandi126 – 133Combined sources8
Helixi134 – 136Combined sources3
Beta strandi138 – 148Combined sources11
Helixi151 – 160Combined sources10
Helixi163 – 171Combined sources9
Helixi181 – 194Combined sources14
Turni195 – 197Combined sources3
Beta strandi206 – 211Combined sources6
Beta strandi214 – 220Combined sources7
Beta strandi228 – 234Combined sources7
Beta strandi254 – 258Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NRGX-ray1.95A1-261[»]
3HY8X-ray2.50A1-261[»]
DisProtiDP00168.
ProteinModelPortaliQ9NVS9.
SMRiQ9NVS9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NVS9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni42 – 45Pyridoxal 5'-phosphate bindingBy similarity4
Regioni225 – 227Pyridoxal 5'-phosphate bindingBy similarity3

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2586. Eukaryota.
COG0259. LUCA.
GeneTreeiENSGT00390000011219.
HOGENOMiHOG000242755.
HOVERGENiHBG045634.
KOiK00275.
OMAiPEHWGGY.
OrthoDBiEOG091G0J0R.
PhylomeDBiQ9NVS9.
TreeFamiTF313411.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851:SF0. PTHR10851:SF0. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NVS9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTCWLRGVTA TFGRPAEWPG YLSHLCGRSA AMDLGPMRKS YRGDREAFEE
60 70 80 90 100
THLTSLDPVK QFAAWFEEAV QCPDIGEANA MCLATCTRDG KPSARMLLLK
110 120 130 140 150
GFGKDGFRFF TNFESRKGKE LDSNPFASLV FYWEPLNRQV RVEGPVKKLP
160 170 180 190 200
EEEAECYFHS RPKSSQIGAV VSHQSSVIPD REYLRKKNEE LEQLYQDQEV
210 220 230 240 250
PKPKSWGGYV LYPQVMEFWQ GQTNRLHDRI VFRRGLPTGD SPLGPMTHRG
260
EEDWLYERLA P
Length:261
Mass (Da):29,988
Last modified:October 1, 2000 - v1
Checksum:i2C74E9F962FE2A95
GO
Isoform 2 (identifier: Q9NVS9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-95: Missing.

Note: No experimental confirmation available.
Show »
Length:166
Mass (Da):19,478
Checksum:i81A7843218C16A1D
GO
Isoform 3 (identifier: Q9NVS9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     122-139: Missing.

Note: No experimental confirmation available.
Show »
Length:243
Mass (Da):27,823
Checksum:i0E1F950A074A37D7
GO
Isoform 4 (identifier: Q9NVS9-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-182: Missing.

Note: No experimental confirmation available.
Show »
Length:218
Mass (Da):25,200
Checksum:i710BED8B9D98115F
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02935850E → K.1 PublicationCorresponds to variant rs549477447dbSNPEnsembl.1
Natural variantiVAR_029359116R → Q.Corresponds to variant rs17679445dbSNPEnsembl.1
Natural variantiVAR_029360229R → W in PNPOD; strong activity decrease. 1 PublicationCorresponds to variant rs104894629dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0564091 – 95Missing in isoform 2. 1 PublicationAdd BLAST95
Alternative sequenceiVSP_056410122 – 139Missing in isoform 3. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_056411140 – 182Missing in isoform 4. 1 PublicationAdd BLAST43

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF468030 mRNA. Translation: AAM76918.1.
AK001397 mRNA. Translation: BAA91668.1.
AK303536 mRNA. Translation: BAG64562.1.
AK303665 mRNA. Translation: BAG64664.1.
AK303792 mRNA. Translation: BAG64749.1.
CH471109 Genomic DNA. Translation: EAW94770.1.
CH471109 Genomic DNA. Translation: EAW94771.1.
BC006525 mRNA. Translation: AAH06525.1.
CCDSiCCDS11522.1. [Q9NVS9-1]
RefSeqiNP_060599.1. NM_018129.3. [Q9NVS9-1]
XP_011523270.1. XM_011524968.2. [Q9NVS9-2]
UniGeneiHs.631742.

Genome annotation databases

EnsembliENST00000225573; ENSP00000225573; ENSG00000108439. [Q9NVS9-1]
ENST00000434554; ENSP00000399960; ENSG00000108439. [Q9NVS9-4]
GeneIDi55163.
KEGGihsa:55163.
UCSCiuc010wlb.3. human. [Q9NVS9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF468030 mRNA. Translation: AAM76918.1.
AK001397 mRNA. Translation: BAA91668.1.
AK303536 mRNA. Translation: BAG64562.1.
AK303665 mRNA. Translation: BAG64664.1.
AK303792 mRNA. Translation: BAG64749.1.
CH471109 Genomic DNA. Translation: EAW94770.1.
CH471109 Genomic DNA. Translation: EAW94771.1.
BC006525 mRNA. Translation: AAH06525.1.
CCDSiCCDS11522.1. [Q9NVS9-1]
RefSeqiNP_060599.1. NM_018129.3. [Q9NVS9-1]
XP_011523270.1. XM_011524968.2. [Q9NVS9-2]
UniGeneiHs.631742.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NRGX-ray1.95A1-261[»]
3HY8X-ray2.50A1-261[»]
DisProtiDP00168.
ProteinModelPortaliQ9NVS9.
SMRiQ9NVS9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120463. 23 interactors.
IntActiQ9NVS9. 2 interactors.
STRINGi9606.ENSP00000225573.

Chemistry databases

BindingDBiQ9NVS9.
ChEMBLiCHEMBL3271932.

PTM databases

iPTMnetiQ9NVS9.
PhosphoSitePlusiQ9NVS9.

Polymorphism and mutation databases

BioMutaiPNPO.
DMDMi37082126.

2D gel databases

REPRODUCTION-2DPAGEIPI00018272.

Proteomic databases

EPDiQ9NVS9.
PaxDbiQ9NVS9.
PeptideAtlasiQ9NVS9.
PRIDEiQ9NVS9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000225573; ENSP00000225573; ENSG00000108439. [Q9NVS9-1]
ENST00000434554; ENSP00000399960; ENSG00000108439. [Q9NVS9-4]
GeneIDi55163.
KEGGihsa:55163.
UCSCiuc010wlb.3. human. [Q9NVS9-1]

Organism-specific databases

CTDi55163.
DisGeNETi55163.
GeneCardsiPNPO.
HGNCiHGNC:30260. PNPO.
HPAiHPA023204.
HPA027776.
MalaCardsiPNPO.
MIMi603287. gene.
610090. phenotype.
neXtProtiNX_Q9NVS9.
OpenTargetsiENSG00000108439.
Orphaneti79096. Pyridoxal phosphate-responsive seizures.
PharmGKBiPA134915565.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2586. Eukaryota.
COG0259. LUCA.
GeneTreeiENSGT00390000011219.
HOGENOMiHOG000242755.
HOVERGENiHBG045634.
KOiK00275.
OMAiPEHWGGY.
OrthoDBiEOG091G0J0R.
PhylomeDBiQ9NVS9.
TreeFamiTF313411.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.
BioCyciMetaCyc:HS03105-MONOMER.
ZFISH:HS03105-MONOMER.
ReactomeiR-HSA-964975. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RKQ9NVS9.

Miscellaneous databases

ChiTaRSiPNPO. human.
EvolutionaryTraceiQ9NVS9.
GeneWikiiPNPO.
GenomeRNAii55163.
PROiQ9NVS9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000108439.
CleanExiHS_PNPO.
ExpressionAtlasiQ9NVS9. baseline and differential.
GenevisibleiQ9NVS9. HS.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851:SF0. PTHR10851:SF0. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPNPO_HUMAN
AccessioniPrimary (citable) accession number: Q9NVS9
Secondary accession number(s): B4E0V0
, B4E152, B4E1D7, D3DTT9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 154 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.