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Q9NVS9 (PNPO_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pyridoxine-5'-phosphate oxidase

EC=1.4.3.5
Alternative name(s):
Pyridoxamine-phosphate oxidase
Gene names
Name:PNPO
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length261 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Ref.6

Catalytic activity

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. HAMAP-Rule MF_01629

Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. HAMAP-Rule MF_01629

Cofactor

Binds 1 FMN per subunit.

Pathway

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP-Rule MF_01629

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.

Subunit structure

Homodimer. Ref.6

Involvement in disease

Pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:610090]: 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,.
Note: The disease is caused by mutations affecting the gene represented in this entry.

Sequence similarities

Belongs to the pyridoxamine 5'-phosphate oxidase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 261261Pyridoxine-5'-phosphate oxidase HAMAP-Rule MF_01629
PRO_0000167783

Regions

Nucleotide binding110 – 1112FMN HAMAP-Rule MF_01629
Nucleotide binding174 – 1752FMN HAMAP-Rule MF_01629
Region225 – 2273Substrate binding HAMAP-Rule MF_01629

Sites

Binding site951FMN
Binding site981FMN; via amide nitrogen
Binding site1001Substrate
Binding site1171FMN
Binding site1571Substrate
Binding site1611Substrate
Binding site1651Substrate

Natural variations

Natural variant501E → K. Ref.7
VAR_029358
Natural variant1161R → Q.
Corresponds to variant rs17679445 [ dbSNP | Ensembl ].
VAR_029359
Natural variant2291R → W in PNPO deficiency; strong activity decrease. Ref.7
Corresponds to variant rs104894629 [ dbSNP | Ensembl ].
VAR_029360

Secondary structure

.................................. 261
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9NVS9 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 2C74E9F962FE2A95

FASTA26129,988
        10         20         30         40         50         60 
MTCWLRGVTA TFGRPAEWPG YLSHLCGRSA AMDLGPMRKS YRGDREAFEE THLTSLDPVK 

        70         80         90        100        110        120 
QFAAWFEEAV QCPDIGEANA MCLATCTRDG KPSARMLLLK GFGKDGFRFF TNFESRKGKE 

       130        140        150        160        170        180 
LDSNPFASLV FYWEPLNRQV RVEGPVKKLP EEEAECYFHS RPKSSQIGAV VSHQSSVIPD 

       190        200        210        220        230        240 
REYLRKKNEE LEQLYQDQEV PKPKSWGGYV LYPQVMEFWQ GQTNRLHDRI VFRRGLPTGD 

       250        260 
SPLGPMTHRG EEDWLYERLA P 

« Hide

References

« Hide 'large scale' references
[1]Kwon O.-S.
Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Brain.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Teratocarcinoma.
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Lymph.
[5]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[6]"Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase."
Musayev F.N., Di Salvo M.L., Ko T.-P., Schirch V., Safo M.K.
Protein Sci. 12:1455-1463(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 49-161 IN COMPLEX WITH FMN AND PYRIDOXAL 5'-PHOSPHATE, PARTIAL PROTEIN SEQUENCE, SUBUNIT, ENZYME REGULATION, FUNCTION.
[7]"Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5'-phosphate oxidase."
Mills P.B., Surtees R.A.H., Champion M.P., Beesley C.E., Dalton N., Scambler P.J., Heales S.J.R., Briddon A., Scheimberg I., Hoffmann G.F., Zschocke J., Clayton P.T.
Hum. Mol. Genet. 14:1077-1086(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT PNPO DEFICIENCY TRP-229, VARIANT LYS-50.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF468030 mRNA. Translation: AAM76918.1.
AK001397 mRNA. Translation: BAA91668.1.
CH471109 Genomic DNA. Translation: EAW94770.1.
CH471109 Genomic DNA. Translation: EAW94771.1.
BC006525 mRNA. Translation: AAH06525.1.
RefSeqNP_060599.1. NM_018129.3.
UniGeneHs.631742.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1NRGX-ray1.95A1-261[»]
3HY8X-ray2.50A1-261[»]
DisProtDP00168.
ProteinModelPortalQ9NVS9.
SMRQ9NVS9. Positions 49-261.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120463. 4 interactions.
STRING9606.ENSP00000225573.

Chemistry

DrugBankDB00114. Pyridoxal Phosphate.

PTM databases

PhosphoSiteQ9NVS9.

Polymorphism databases

DMDM37082126.

2D gel databases

REPRODUCTION-2DPAGEIPI00018272.

Proteomic databases

PaxDbQ9NVS9.
PeptideAtlasQ9NVS9.
PRIDEQ9NVS9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000225573; ENSP00000225573; ENSG00000108439.
GeneID55163.
KEGGhsa:55163.
UCSCuc002imo.3. human.

Organism-specific databases

CTD55163.
GeneCardsGC17P046018.
HGNCHGNC:30260. PNPO.
HPAHPA023204.
HPA027776.
MIM603287. gene.
610090. phenotype.
neXtProtNX_Q9NVS9.
Orphanet79096. Pyridoxal phosphate-responsive seizures.
PharmGKBPA134915565.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0259.
HOGENOMHOG000242755.
HOVERGENHBG045634.
InParanoidQ9NVS9.
KOK00275.
OMAPEHWGGY.
PhylomeDBQ9NVS9.
TreeFamTF313411.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.
REACT_116125. Disease.
SABIO-RKQ9NVS9.
UniPathwayUPA00190; UER00304.
UPA00190; UER00305.

Gene expression databases

ArrayExpressQ9NVS9.
BgeeQ9NVS9.
CleanExHS_PNPO.
GenevestigatorQ9NVS9.

Family and domain databases

Gene3D2.30.110.10. 1 hit.
HAMAPMF_01629. PdxH.
InterProIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERPTHR10851. PTHR10851. 1 hit.
PfamPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMSSF50475. SSF50475. 1 hit.
TIGRFAMsTIGR00558. pdxH. 1 hit.
PROSITEPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPNPO. human.
EvolutionaryTraceQ9NVS9.
GeneWikiPNPO.
GenomeRNAi55163.
NextBio58925.
PROQ9NVS9.
SOURCESearch...

Entry information

Entry namePNPO_HUMAN
AccessionPrimary (citable) accession number: Q9NVS9
Secondary accession number(s): D3DTT9
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM