Pyridoxine-5'-phosphate oxidase - Homo sapiens (Human)

Names and origin

Protein names

Recommended name:
    Pyridoxine-5'-phosphate oxidase
    EC=1.4.3.5
Alternative name(s):
    Pyridoxamine-phosphate oxidase

Gene names

Name:

PNPO

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	261 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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. Pyridoxine 5'-phosphate + O₂ = pyridoxal 5'-phosphate + H₂O₂.
Cofactor	Binds 1 FMN per subunit.
Pathway	Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
Subunit structure	Homodimer. Ref.6
Involvement in 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,.
Sequence similarities	Belongs to the pyridoxamine 5'-phosphate oxidase family.

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Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Coding sequence diversity	Polymorphism
Disease	Disease mutation Epilepsy
Ligand	FMN Flavoprotein Pyridoxal phosphate
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW pyridoxine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	FMN binding Inferred from electronic annotation. Source: InterPro pyridoxamine-phosphate oxidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 261

261

Pyridoxine-5'-phosphate oxidase

PRO_0000167783

Regions

Nucleotide binding

110 – 111

2

FMN

Nucleotide binding

174 – 175

2

FMN

Region

225 – 227

3

Substrate binding

Sites

Binding site

95

1

FMN

Binding site

98

1

FMN; via amide nitrogen

Binding site

100

1

Substrate

Binding site

117

1

FMN

Binding site

157

1

Substrate

Binding site

161

1

Substrate

Binding site

165

1

Substrate

Amino acid modifications

Modified residue

40

1

Phosphoserine Ref.4

Modified residue

165

1

Phosphoserine By similarity

Modified residue

241

1

Phosphoserine By similarity

Natural variations

Natural variant

50

1

E → K Ref.7

VAR_029358

Natural variant

116

1

R → Q: dbSNP rs17679445.

VAR_029359

Natural variant

229

1

R → W in PNPO deficiency; strong activity decrease.

VAR_029360

Secondary structure

1

.

261

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9NVS9-1 [UniParc].

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

FASTA

261

29,988

        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

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References

	« Hide 'large scale' referencesShow '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. Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Teratocarcinoma.
[3]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lymph.
[4]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-40, MASS SPECTROMETRY.
[5]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[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: 12824491] [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: 15772097] [Abstract] Cited for: VARIANT PNPO DEFICIENCY TRP-229, VARIANT LYS-50.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

AF468030 mRNA. Translation: AAM76918.1.
AK001397 mRNA. Translation: BAA91668.1.
BC006525 mRNA. Translation: AAH06525.1.

IPI

IPI00018272.

RefSeq

NP_060599.1.

UniGene

Hs.631742

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NRG	X-ray	1.95	A	1-261	[»]

DisProt

DP00168.

ModBase

Search...

PTM databases

PhosphoSite

Q9NVS9.

2-D gel databases

REPRODUCTION-2DPAGE

IPI00018272.

Proteomic databases

PeptideAtlas

Q9NVS9.

PRIDE

Q9NVS9.

Genome annotation databases

Ensembl

ENSG00000108439. Homo sapiens. [Contig view]

GeneID

55163.

KEGG

hsa:55163.

NMPDR

fig|9606.3.peg.13977.

UCSC

uc002imo.1. human.

Organism-specific databases

GeneCards

GC17P043373.

H-InvDB

HIX0013930.

HGNC

HGNC:30260. PNPO.

MIM

603287. gene.
610090. phenotype.

Orphanet

1934. Early infantile epileptic encephalopathy.

PharmGKB

PA134915565.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q9NVS9.

HOVERGEN

Q9NVS9.

OMA

Q9NVS9. FTFFTNY.

Enzyme and pathway databases

BRENDA

1.4.3.5. 247.

Gene expression databases

ArrayExpress

Q9NVS9.

Bgee

Q9NVS9.

CleanEx

HS_PNPO.

GermOnline

ENSG00000108439. Homo sapiens.

Family and domain databases

InterPro

IPR011576. PNPOx_rel_FMN_bd_core.
IPR000659. Pyridoxamine_oxidase.
IPR019740. Pyridoxamine_oxidase_CS.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN_bd.
[Graphical view]

Gene3D

G3DSA:2.30.110.10. PNPOx_FMN_bd. 1 hit.

PANTHER

PTHR10851. Pyridox_oxidase. 1 hit.

Pfam

PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]

ProDom

PD006312. Pyridox_oxidase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR00558. pdxH. 1 hit.

PROSITE

PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00114. Pyridoxal Phosphate.

NextBio

58925.

SOURCE

Search...

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Entry information

Entry name

PNPO_HUMAN

Accession

Primary (citable) accession number: Q9NVS9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 26, 2003
Last sequence update:	October 1, 2000
Last modified:	July 7, 2009
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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