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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343)
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: 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 sitei88SubstrateUniRule annotation1
Binding sitei104FMNUniRule annotation1
Binding sitei105FMNUniRule annotation1
Binding sitei127FMNUniRule annotation1
Binding sitei145SubstrateUniRule annotation1
Binding sitei149SubstrateUniRule annotation1
Binding sitei153SubstrateUniRule annotation1
Binding sitei207FMNUniRule annotation1
Binding sitei217FMNUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi83 – 88FMNUniRule annotation6
Nucleotide bindingi98 – 99FMNUniRule annotation2
Nucleotide bindingi162 – 163FMNUniRule annotation2

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

BioCyciBFRA272559:GKF0-1321-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:BF1385
OrganismiBacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343)
Taxonomic identifieri272559 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesBacteroidaceaeBacteroides
Proteomesi
  • UP000006731 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001676821 – 235Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST235

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi272559.BF1385.

Structurei

3D structure databases

ProteinModelPortaliQ5LFJ5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 33Substrate bindingUniRule annotation4
Regioni213 – 215Substrate bindingUniRule annotation3

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
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:SF0. PTHR10851:SF0. 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.

Q5LFJ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTDHVSTHP DSPLHGNGIG SEAINLAAIR QEYTKGGLKE GDLPDNPLSL
60 70 80 90 100
FNRWLHEAID AQVDEPTAML VGTVSPEGQP STRTVLLKDL HDGKFIFYTN
110 120 130 140 150
YESRKGTHLA KNPYISLSFV WHALERQVHI EGIASKVPAG ESDTYFRQRP
160 170 180 190 200
YKSRIGARIS PQSRPLKSRM QLIRNFVAEA ARWVGREVER PAHWGGYAVT
210 220 230
PHRIEFWQGR ANRLHDRFLY SLQPDGSWQK ERLAP
Length:235
Mass (Da):26,673
Last modified:June 21, 2005 - v1
Checksum:i6C6C85CC8E160374
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR626927 Genomic DNA. Translation: CAH07098.1.

Genome annotation databases

EnsemblBacteriaiCAH07098; CAH07098; BF9343_1317.
KEGGibfs:BF9343_1317.
PATRICi21039212. VBIBacFra29119_1355.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR626927 Genomic DNA. Translation: CAH07098.1.

3D structure databases

ProteinModelPortaliQ5LFJ5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272559.BF1385.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAH07098; CAH07098; BF9343_1317.
KEGGibfs:BF9343_1317.
PATRICi21039212. VBIBacFra29119_1355.

Phylogenomic databases

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.
BioCyciBFRA272559:GKF0-1321-MONOMER.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
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:SF0. PTHR10851:SF0. 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...

Entry informationi

Entry nameiPDXH_BACFN
AccessioniPrimary (citable) accession number: Q5LFJ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: June 21, 2005
Last modified: November 2, 2016
This is version 76 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

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 one 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.