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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Paracoccus denitrificans (strain Pd 1222)
Status
Reviewed-Annotation score: -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: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei54SubstrateUniRule annotation1
Binding sitei75FMNUniRule annotation1
Binding sitei97FMNUniRule annotation1
Binding sitei115SubstrateUniRule annotation1
Binding sitei119SubstrateUniRule annotation1
Binding sitei123SubstrateUniRule annotation1
Binding sitei176FMNUniRule annotation1
Binding sitei186FMNUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi49 – 54FMNUniRule annotation6
Nucleotide bindingi68 – 69FMNUniRule annotation2
Nucleotide bindingi132 – 133FMNUniRule annotation2

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processPyridoxine biosynthesis
LigandFlavoprotein, FMN

Enzyme and pathway databases

BioCyciPDEN318586:G1GW1-864-MONOMER
UniPathwayiUPA01068; UER00304
UPA01068; 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:Pden_0858
OrganismiParacoccus denitrificans (strain Pd 1222)
Taxonomic identifieri318586 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus
Proteomesi
  • UP000000361 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002923121 – 220Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST220

Proteomic databases

PRIDEiA1B0C6

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi318586.Pden_0858

Structurei

3D structure databases

ProteinModelPortaliA1B0C6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni182 – 184Substrate bindingUniRule annotation3

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4108S7T Bacteria
COG0259 LUCA
HOGENOMiHOG000242755
KOiK00275
OMAiPEPNAMV
OrthoDBiPOG091H054N

Family and domain databases

Gene3Di2.30.110.10, 1 hit
HAMAPiMF_01629 PdxH, 1 hit
InterProiView protein in InterPro
IPR000659 Pyridox_Oxase
IPR019740 Pyridox_Oxase_CS
IPR011576 Pyridox_Oxase_put
IPR019576 Pyridoxamine_oxidase_dimer_C
IPR012349 Split_barrel_FMN-bd
PANTHERiPTHR10851:SF0 PTHR10851:SF0, 1 hit
PfamiView protein in Pfam
PF10590 PNP_phzG_C, 1 hit
PF01243 Putative_PNPOx, 1 hit
PIRSFiPIRSF000190 Pyd_amn-ph_oxd, 1 hit
TIGRFAMsiTIGR00558 pdxH, 1 hit
PROSITEiView protein in PROSITE
PS01064 PYRIDOX_OXIDASE, 1 hit

Sequencei

Sequence statusi: Complete.

A1B0C6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDRGGIFAG DDPFAIARSW LAEAERTEPN DANAMALATV DADGLPDARM
60 70 80 90 100
VLLKDIEGGA ADGSFVFYTN YESAKGVEIE ATGVAAFVMH WKSLRRQIRV
110 120 130 140 150
RGHVTRVEPE LADAYYASRP LQSRIGAWAS RQSRPLASRG ALMAEVARLG
160 170 180 190 200
ISLGLNPSRP PHWGGYRIHP VQIEFWADGA FRLHDRFRWT KSSYQGENSA
210 220
LRDEGQEVPQ SLWQVCRLSP
Length:220
Mass (Da):24,399
Last modified:January 23, 2007 - v1
Checksum:i8915762E0887AAA9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000489 Genomic DNA Translation: ABL68970.1
RefSeqiWP_011747198.1, NC_008686.1

Genome annotation databases

EnsemblBacteriaiABL68970; ABL68970; Pden_0858
KEGGipde:Pden_0858

Similar proteinsi

Entry informationi

Entry nameiPDXH_PARDP
AccessioniPrimary (citable) accession number: A1B0C6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 70 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health