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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Polaromonas naphthalenivorans (strain CJ2)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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

Catalytic activityi

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

Cofactori

FMNUniRule annotationNote: Binds 1 FMN per subunit.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei64 – 641FMNUniRule annotation
Binding sitei67 – 671FMN; via amide nitrogenUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Binding sitei86 – 861FMNUniRule annotation
Binding sitei126 – 1261SubstrateUniRule annotation
Binding sitei130 – 1301SubstrateUniRule annotation
Binding sitei134 – 1341SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi79 – 802FMNUniRule annotation
Nucleotide bindingi143 – 1442FMNUniRule annotation

GO - Molecular functioni

  1. FMN binding Source: UniProtKB-HAMAP
  2. pyridoxamine-phosphate oxidase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciPNAP365044:GJ8X-3035-MONOMER.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidaseUniRule annotation (EC:1.4.3.5UniRule annotation)
Alternative name(s):
PNP/PMP oxidaseUniRule annotation
Short name:
PNPOxUniRule annotation
Pyridoxal 5'-phosphate synthaseUniRule annotation
Gene namesi
Name:pdxHUniRule annotation
Ordered Locus Names:Pnap_2989
OrganismiPolaromonas naphthalenivorans (strain CJ2)
Taxonomic identifieri365044 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaePolaromonas
ProteomesiUP000000644: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 215215Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000292313Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi365044.Pnap_2989.

Structurei

3D structure databases

ProteinModelPortaliA1VRL0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 144Substrate bindingUniRule annotation
Regioni193 – 1953Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the pyridoxamine 5'-phosphate oxidase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 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.

Sequencei

Sequence statusi: Complete.

A1VRL0-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSSPTSIADL RKSYERAELN EDASHADPLN QFDQWLNEAI SAQVPEPNAM
60 70 80 90 100
TLATVASNLR PSTRVVLIKG FDAQGIVWYT NYASRKGLEL AGNPYAALQF
110 120 130 140 150
HWVELERVVR IEGVVEKVSD EESDAYFHSR PLDSRIGAWA SPQSEVISGR
160 170 180 190 200
GVLLANAAKF GAKFMLQPPR PAHWGGYRLK PDNWQFWQGR KSRLHDRLRY
210
TLQGDAGWLR ERLAP
Length:215
Mass (Da):24,289
Last modified:February 6, 2007 - v1
Checksum:i097D55265C7A8DF4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000529 Genomic DNA. Translation: ABM38288.1.
RefSeqiWP_011802362.1. NC_008781.1.
YP_983209.1. NC_008781.1.

Genome annotation databases

EnsemblBacteriaiABM38288; ABM38288; Pnap_2989.
GeneIDi4688886.
KEGGipna:Pnap_2989.
PATRICi22950681. VBIPolNap76733_3864.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000529 Genomic DNA. Translation: ABM38288.1.
RefSeqiWP_011802362.1. NC_008781.1.
YP_983209.1. NC_008781.1.

3D structure databases

ProteinModelPortaliA1VRL0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi365044.Pnap_2989.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABM38288; ABM38288; Pnap_2989.
GeneIDi4688886.
KEGGipna:Pnap_2989.
PATRICi22950681. VBIPolNap76733_3864.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciPNAP365044:GJ8X-3035-MONOMER.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 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.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CJ2.

Entry informationi

Entry nameiPDXH_POLNA
AccessioniPrimary (citable) accession number: A1VRL0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: February 6, 2007
Last modified: February 4, 2015
This is version 54 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.