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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Xylella fastidiosa (strain 9a5c)
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 sitei58SubstrateUniRule annotation1
Binding sitei75FMNUniRule annotation1
Binding sitei100FMNUniRule annotation1
Binding sitei118SubstrateUniRule annotation1
Binding sitei122SubstrateUniRule annotation1
Binding sitei126SubstrateUniRule annotation1
Binding sitei180FMNUniRule annotation1
Binding sitei190FMNUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi53 – 58FMNUniRule annotation6
Nucleotide bindingi68 – 69FMNUniRule annotation2
Nucleotide bindingi135 – 136FMNUniRule annotation2

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processPyridoxine biosynthesis
LigandFlavoprotein, FMN

Enzyme and pathway databases

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:XF_1337
OrganismiXylella fastidiosa (strain 9a5c)
Taxonomic identifieri160492 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
Proteomesi
  • UP000000812 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001677771 – 208Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST208

Proteomic databases

PRIDEiQ9PDP2

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi160492.XF1337

Structurei

3D structure databases

ProteinModelPortaliQ9PDP2
SMRiQ9PDP2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni186 – 188Substrate bindingUniRule annotation3

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4108S7T Bacteria
COG0259 LUCA
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.

Q9PDP2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIFPCLFQSM LNLYAEALST FSLLFEEAKS SSEIEPDAMM LATASLEGHP
60 70 80 90 100
SVRTVLLKKF DARGFVFYSH IDSPKGRDLQ ANPQAALLFL WRSLREAGVQ
110 120 130 140 150
VRIEGRVQQV LAEEADAYFA SRPRQSQIGA WASMQSCPLG SPEEFQARLA
160 170 180 190 200
EVKATFEGRD VPRPEGWVGF RVAPRVLEFW YGARFRLHER WRYEVDAAGY

WRKFLLYP
Length:208
Mass (Da):23,832
Last modified:October 1, 2000 - v1
Checksum:i7A5A94AA338AF5CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003849 Genomic DNA Translation: AAF84146.1
PIRiF82693

Genome annotation databases

EnsemblBacteriaiAAF84146; AAF84146; XF_1337
KEGGixfa:XF_1337

Similar proteinsi

Entry informationi

Entry nameiPDXH_XYLFA
AccessioniPrimary (citable) accession number: Q9PDP2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: October 1, 2000
Last modified: May 23, 2018
This is version 101 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