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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Frankia sp. (strain CcI3)
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 sitei75 – 751FMNUniRule annotation
Binding sitei78 – 781FMN; via amide nitrogenUniRule annotation
Binding sitei80 – 801SubstrateUniRule annotation
Binding sitei97 – 971FMNUniRule annotation
Binding sitei137 – 1371SubstrateUniRule annotation
Binding sitei141 – 1411SubstrateUniRule annotation
Binding sitei145 – 1451SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi90 – 912FMNUniRule annotation
Nucleotide bindingi154 – 1552FMNUniRule 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

BioCyciFSP106370:GI1F-80-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:Francci3_0079
OrganismiFrankia sp. (strain CcI3)
Taxonomic identifieri106370 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesFrankineaeFrankiaceaeFrankia
ProteomesiUP000001937: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 267267Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000255868Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi106370.Francci3_0079.

Structurei

3D structure databases

ProteinModelPortaliQ2JGW9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni20 – 234Substrate bindingUniRule annotation
Regioni206 – 2083Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OrthoDBiEOG60KN2Z.

Family and domain databases

Gene3Di2.30.110.10. 2 hits.
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]
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q2JGW9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGGPDPDVPD LDVPDPALLR QGYRAGRLEP EHLAPTWVEQ FAAWFIDAAT
60 70 80 90 100
PGVGVPEANA AVFATASAAG RPSARTVLLK GFDQRGFVIY TNYASRKGRE
110 120 130 140 150
ATENPFGSLV FPWYALERQV VVIGSIERVS RAETERYFQS RPHGSQLGAW
160 170 180 190 200
ASHQSTIIES RTVLDDRAAE LAARWPEGTR VPTPEFWGGL RIVPDTVEFW
210 220 230 240 250
QGRADRLHDR LRYRRVSVPA DGGGTDSLAV ADPDATGVRV GDAGGGDAGG
260
GVPTAAEDLW VVERLAP
Length:267
Mass (Da):28,842
Last modified:October 31, 2006 - v2
Checksum:i61D9293782A71111
GO

Sequence cautioni

The sequence ABD09473.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD09473.1. Different initiation.
RefSeqiYP_479202.1. NC_007777.1.

Genome annotation databases

EnsemblBacteriaiABD09473; ABD09473; Francci3_0079.
GeneIDi3905123.
KEGGifra:Francci3_0079.
PATRICi21922900. VBIFraSp10456_0087.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD09473.1. Different initiation.
RefSeqiYP_479202.1. NC_007777.1.

3D structure databases

ProteinModelPortaliQ2JGW9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi106370.Francci3_0079.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD09473; ABD09473; Francci3_0079.
GeneIDi3905123.
KEGGifra:Francci3_0079.
PATRICi21922900. VBIFraSp10456_0087.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciFSP106370:GI1F-80-MONOMER.

Family and domain databases

Gene3Di2.30.110.10. 2 hits.
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]
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: CcI3.

Entry informationi

Entry nameiPDXH_FRASC
AccessioniPrimary (citable) accession number: Q2JGW9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: October 31, 2006
Last modified: January 7, 2015
This is version 64 of the entry and version 2 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.