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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Agrobacterium radiobacter (strain K84 / ATCC BAA-868)
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 sitei53 – 531FMNUniRule annotation
Binding sitei56 – 561FMN; via amide nitrogenUniRule annotation
Binding sitei58 – 581SubstrateUniRule annotation
Binding sitei75 – 751FMNUniRule annotation
Binding sitei115 – 1151SubstrateUniRule annotation
Binding sitei119 – 1191SubstrateUniRule annotation
Binding sitei123 – 1231SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi68 – 692FMNUniRule annotation
Nucleotide bindingi132 – 1332FMNUniRule 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

BioCyciARAD311403:GHU8-942-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:Arad_1220
OrganismiAgrobacterium radiobacter (strain K84 / ATCC BAA-868)
Taxonomic identifieri311403 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
ProteomesiUP000001600 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 206206Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_1000186285Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi311403.Arad_1220.

Structurei

3D structure databases

ProteinModelPortaliB9JAN3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni183 – 1853Substrate 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.

B9JAN3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSENELTSGD FTEQNEPFAL FAAWLREAEA TEPNDPNAVA LATVDKDGLP
60 70 80 90 100
NVRMVLLKGF DSQGFVFYTN FESQKGQEIL SQKKAAMCFH WKSLRRQVRL
110 120 130 140 150
RGLVEVVSDK EADEYYKTRA RGSRIGAWAS KQSRPLEGRF ALEKAVAEYT
160 170 180 190 200
ARYALGDIPR PPHWSGFRIR PLSIEFWHDR PFRLHDRVEF RREVPEGAWE

KVRMYP
Length:206
Mass (Da):23,898
Last modified:March 23, 2009 - v1
Checksum:iA7C543A00B6ACD94
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000628 Genomic DNA. Translation: ACM25716.1.
RefSeqiYP_002543642.1. NC_011985.1.

Genome annotation databases

EnsemblBacteriaiACM25716; ACM25716; Arad_1220.
KEGGiara:Arad_1220.
PATRICi20802622. VBIAgrRad129173_3418.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000628 Genomic DNA. Translation: ACM25716.1.
RefSeqiYP_002543642.1. NC_011985.1.

3D structure databases

ProteinModelPortaliB9JAN3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi311403.Arad_1220.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACM25716; ACM25716; Arad_1220.
KEGGiara:Arad_1220.
PATRICi20802622. VBIAgrRad129173_3418.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiEYTARYA.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciARAD311403:GHU8-942-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: K84 / ATCC BAA-868.

Entry informationi

Entry nameiPDXH_AGRRK
AccessioniPrimary (citable) accession number: B9JAN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 27, 2009
Last sequence update: March 23, 2009
Last modified: March 31, 2015
This is version 42 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.