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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Dichelobacter nodosus (strain VCS1703A)
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 sitei61 – 611FMNUniRule annotation
Binding sitei64 – 641FMN; via amide nitrogenUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Binding sitei83 – 831FMNUniRule annotation
Binding sitei123 – 1231SubstrateUniRule annotation
Binding sitei127 – 1271SubstrateUniRule annotation
Binding sitei131 – 1311SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi76 – 772FMNUniRule annotation
Nucleotide bindingi140 – 1412FMNUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciDNOD246195:GHHS-1020-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:DNO_1023
OrganismiDichelobacter nodosus (strain VCS1703A)
Taxonomic identifieri246195 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaCardiobacterialesCardiobacteriaceaeDichelobacter
ProteomesiUP000000248 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 212212Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000335783Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi246195.DNO_1023.

Structurei

3D structure databases

ProteinModelPortaliA5EXX0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni191 – 1933Substrate 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.
IPR019740. Pyridox_Oxase_CS.
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.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A5EXX0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDIGSIRHDF TEHPPLLEQD LAADPIEQFA AWFQYAVDSG ISEPNGFVLA
60 70 80 90 100
TVAADGQPSQ RSVLLKLFDE EGFVFYTNYS SQKAEEIEKN AQVSMSFPWY
110 120 130 140 150
ALQRQIHVYG RAEKIPREQS LAYFLTRPQG SQIGAWASPQ SKIIESRDFL
160 170 180 190 200
MLKWQNMKAK FHEGKIPLPD FWGGYRVRPH KIEFWQGQPS RLHDRFLYEK
210
TENGWTVSRR AP
Length:212
Mass (Da):24,570
Last modified:June 12, 2007 - v1
Checksum:iC8C9F5F3B890DFE5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ13205.1.
RefSeqiWP_012031335.1. NC_009446.1.
YP_001209911.1. NC_009446.1.

Genome annotation databases

EnsemblBacteriaiABQ13205; ABQ13205; DNO_1023.
KEGGidno:DNO_1023.
PATRICi21786386. VBIDicNod48475_1021.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ13205.1.
RefSeqiWP_012031335.1. NC_009446.1.
YP_001209911.1. NC_009446.1.

3D structure databases

ProteinModelPortaliA5EXX0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246195.DNO_1023.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ13205; ABQ13205; DNO_1023.
KEGGidno:DNO_1023.
PATRICi21786386. VBIDicNod48475_1021.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciDNOD246195:GHHS-1020-MONOMER.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
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. 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.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VCS1703A.

Entry informationi

Entry nameiPDXH_DICNV
AccessioniPrimary (citable) accession number: A5EXX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: June 12, 2007
Last modified: April 29, 2015
This is version 60 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.