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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Leptospira borgpetersenii serovar Hardjo-bovis (strain L550)
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

Pathway: B6 vitamer interconversion

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 B6 vitamer interconversion, which is itself part of Cofactor biosynthesis.
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 B6 vitamer interconversion and in Cofactor biosynthesis.

Pathway: B6 vitamer interconversion

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 B6 vitamer interconversion, which is itself part of Cofactor biosynthesis.
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 B6 vitamer interconversion and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei62 – 621FMNUniRule annotation
Binding sitei65 – 651FMN; via amide nitrogenUniRule annotation
Binding sitei67 – 671SubstrateUniRule annotation
Binding sitei84 – 841FMNUniRule annotation
Binding sitei124 – 1241SubstrateUniRule annotation
Binding sitei128 – 1281SubstrateUniRule annotation
Binding sitei132 – 1321SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi77 – 782FMNUniRule annotation
Nucleotide bindingi141 – 1422FMNUniRule 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

BioCyciLBOR355276:GHUQ-2115-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:LBL_2135
OrganismiLeptospira borgpetersenii serovar Hardjo-bovis (strain L550)
Taxonomic identifieri355276 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesLeptospiralesLeptospiraceaeLeptospira

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 214214Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000292300Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi355276.LBL_2135.

Structurei

3D structure databases

ProteinModelPortaliQ04ZE7.
SMRiQ04ZE7. Positions 22-214.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 124Substrate bindingUniRule annotation
Regioni192 – 1943Substrate 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.

Q04ZE7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSKISEIRK NYSLSSLDIG DIGDDPISFF QKWFEEAVLS EVLEVNAMTL
60 70 80 90 100
ATATKDGKPN ARIVLLKEIL EDSFVFYTNY ESKKGRELEE NPRACLVFFW
110 120 130 140 150
SELERQVRIE GGVKKVSREE SNVYFHSRPR GSQIGAVVSP QSYEIPNRKF
160 170 180 190 200
LEERFEEFSK LYEGKEVDLP NHWGGYAVHP NRIEFWQGRS SRLHDRIVFE
210
KDTDSSWKKF RVAP
Length:214
Mass (Da):24,950
Last modified:November 14, 2006 - v1
Checksum:i475A47F0692627DC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000348 Genomic DNA. Translation: ABJ79548.1.
RefSeqiWP_011670589.1. NC_008508.1.
YP_798481.1. NC_008508.1.

Genome annotation databases

EnsemblBacteriaiABJ79548; ABJ79548; LBL_2135.
GeneIDi4406893.
KEGGilbl:LBL_2135.
PATRICi22368542. VBILepBor75619_2723.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000348 Genomic DNA. Translation: ABJ79548.1.
RefSeqiWP_011670589.1. NC_008508.1.
YP_798481.1. NC_008508.1.

3D structure databases

ProteinModelPortaliQ04ZE7.
SMRiQ04ZE7. Positions 22-214.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi355276.LBL_2135.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ79548; ABJ79548; LBL_2135.
GeneIDi4406893.
KEGGilbl:LBL_2135.
PATRICi22368542. VBILepBor75619_2723.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciLBOR355276:GHUQ-2115-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: L550.

Entry informationi

Entry nameiPDXH_LEPBL
AccessioniPrimary (citable) accession number: Q04ZE7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: November 14, 2006
Last modified: June 24, 2015
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.