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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Brucella abortus (strain 2308)
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 sitei55 – 551FMNUniRule annotation
Binding sitei58 – 581FMN; via amide nitrogenUniRule annotation
Binding sitei60 – 601SubstrateUniRule annotation
Binding sitei77 – 771FMNUniRule annotation
Binding sitei117 – 1171SubstrateUniRule annotation
Binding sitei121 – 1211SubstrateUniRule annotation
Binding sitei125 – 1251SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi70 – 712FMNUniRule annotation
Nucleotide bindingi134 – 1352FMNUniRule 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

BioCyciBABO359391:GKDV-451-MONOMER.
BMEL359391:GJOQ-451-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:BAB1_0444
OrganismiBrucella abortus (strain 2308)
Taxonomic identifieri359391 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
ProteomesiUP000002719 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000255856Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ2YMD1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni185 – 1873Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiEYTARYA.
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.

Q2YMD1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEPVKMTNSS DDFTQSAEPF KLFAEWLADA AKSEPNDPNA VALATVDPDG
60 70 80 90 100
LPNVRMVLLK DFDETGFVFY TNYESKKGQE ILSAEKAAMC FHWKSLRRQV
110 120 130 140 150
RVRGPVEKVS DAEADAYYAS RPRGSRIGAW ASKQSRPLES RFALEKAVAE
160 170 180 190 200
YTAKYAIGDI PRPPYWSGFR IRPVSIEFWH DRPFRLHDRV LFTRPTPEGD

WNKDRLYP
Length:208
Mass (Da):23,866
Last modified:February 7, 2006 - v1
Checksum:iCB1F50BC9612DE28
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM040264 Genomic DNA. Translation: CAJ10400.1.
RefSeqiWP_002963574.1. NC_007618.1.
YP_413904.1. NC_007618.1.

Genome annotation databases

EnsemblBacteriaiCAJ10400; CAJ10400; BAB1_0444.
KEGGibmf:BAB1_0444.
PATRICi17843760. VBIBruMel86222_0465.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM040264 Genomic DNA. Translation: CAJ10400.1.
RefSeqiWP_002963574.1. NC_007618.1.
YP_413904.1. NC_007618.1.

3D structure databases

ProteinModelPortaliQ2YMD1.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAJ10400; CAJ10400; BAB1_0444.
KEGGibmf:BAB1_0444.
PATRICi17843760. VBIBruMel86222_0465.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiEYTARYA.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciBABO359391:GKDV-451-MONOMER.
BMEL359391:GJOQ-451-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: 2308.

Entry informationi

Entry nameiPDXH_BRUA2
AccessioniPrimary (citable) accession number: Q2YMD1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: February 7, 2006
Last modified: June 24, 2015
This is version 66 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. Brucella abortus strain 2308
    Brucella abortus (strain 2308): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.