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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei48 – 481FMNUniRule annotation
Binding sitei51 – 511FMN; via amide nitrogenUniRule annotation
Binding sitei53 – 531SubstrateUniRule annotation
Binding sitei70 – 701FMNUniRule annotation
Binding sitei110 – 1101SubstrateUniRule annotation
Binding sitei114 – 1141SubstrateUniRule annotation
Binding sitei118 – 1181SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi63 – 642FMNUniRule annotation
Nucleotide bindingi127 – 1282FMNUniRule annotation

GO - Molecular functioni

  1. FMN binding Source: UniProtKB-HAMAP
  2. pyridoxamine-phosphate oxidase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciRSPH272943:GJAS-959-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:RHOS4_09330
ORF Names:RSP_2345
OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Taxonomic identifieri272943 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
ProteomesiUP000002703: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 200200Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000255881Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi272943.RSP_2345.

Structurei

3D structure databases

ProteinModelPortaliQ3J3Y3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni177 – 1793Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiFTNRESR.
OrthoDBiEOG60KN2Z.
PhylomeDBiQ3J3Y3.

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.

Q3J3Y3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDRTGIFAGD DPFAIAAGWL AEAEPQEPND PNAIALATVD AAGLPNVRMV
60 70 80 90 100
LLKEIEAEAF VFYTNYGSQK AVEIETSGKA AFVLHWKSLR RQIRVRGLVE
110 120 130 140 150
REEGAQADAY YASRSLKSRL GAWASEQSRP LASRTSLLAE VARVTARFGT
160 170 180 190 200
NPPRPAFWGG FRIRPLEIEF WADGAFRLHD RFRWRRNSLS DGWSIERLNP
Length:200
Mass (Da):22,449
Last modified:November 8, 2005 - v1
Checksum:iC96149CF03AF38B7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000143 Genomic DNA. Translation: ABA78501.1.
RefSeqiYP_352402.1. NC_007493.2.

Genome annotation databases

EnsemblBacteriaiABA78501; ABA78501; RSP_2345.
GeneIDi3719878.
KEGGirsp:RSP_2345.
PATRICi23151731. VBIRhoSph57909_1259.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000143 Genomic DNA. Translation: ABA78501.1.
RefSeqiYP_352402.1. NC_007493.2.

3D structure databases

ProteinModelPortaliQ3J3Y3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272943.RSP_2345.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA78501; ABA78501; RSP_2345.
GeneIDi3719878.
KEGGirsp:RSP_2345.
PATRICi23151731. VBIRhoSph57909_1259.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiFTNRESR.
OrthoDBiEOG60KN2Z.
PhylomeDBiQ3J3Y3.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciRSPH272943:GJAS-959-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. "Complete sequence of chromosome 1 of Rhodobacter sphaeroides 2.4.1."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.

Entry informationi

Entry nameiPDXH_RHOS4
AccessioniPrimary (citable) accession number: Q3J3Y3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 8, 2005
Last modified: February 4, 2015
This is version 68 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

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.