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Reviewed, UniProtKB/Swiss-Prot Q89RY8 (PDXH_BRAJA)

Last modified February 9, 2010. Version 47. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Pyridoxine/pyridoxamine 5'-phosphate oxidase
    EC=1.4.3.5
Alternative name(s):
    PNP/PMP oxidase
      Short name=PNPOx
    Pyridoxal 5'-phosphate synthase
Gene names
Name: pdxH
Ordered Locus Names: bll2624
OrganismBradyrhizobium japonicum [Complete proteome] [HAMAP]
Taxonomic identifier375 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

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Protein attributes

Sequence length213 AA.
Sequence statusComplete.
Protein existenceInferred from homology.

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General annotation (Comments)

Function

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP) By similarity. HAMAP MF_01629

Catalytic activity

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. HAMAP MF_01629

Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. HAMAP MF_01629

Cofactor

Binds 1 FMN per subunit By similarity. HAMAP MF_01629

Pathway

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP MF_01629

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.

Subunit structure

Homodimer By similarity. HAMAP MF_01629

Sequence similarities

Belongs to the pyridoxamine 5'-phosphate oxidase family.

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Ontologies

Keywords
   Biological processPyridoxine biosynthesis
   LigandFMN
Flavoprotein
   Molecular functionOxidoreductase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processoxidation reduction

Inferred from electronic annotation. Source: UniProtKB-KW

pyridoxine biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functionFMN binding

Inferred from electronic annotation. Source: HAMAP

pyridoxamine-phosphate oxidase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 213213Pyridoxine/pyridoxamine 5'-phosphate oxidase HAMAP MF_01629
PRO_0000167692

Regions

Nucleotide binding75 – 762FMN By similarity
Nucleotide binding139 – 1402FMN By similarity
Region190 – 1923Substrate binding By similarity

Sites

Binding site601FMN By similarity
Binding site631FMN; via amide nitrogen By similarity
Binding site651Substrate By similarity
Binding site821FMN By similarity
Binding site1221Substrate By similarity
Binding site1261Substrate By similarity

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Sequences

Sequence LengthMass (Da)Tools
Q89RY8-1 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: D12CF55C86CFBFB6

FASTA21324,181
        10         20         30         40         50         60 
MTDTTSMKHQ TPLTSGDFTA ADEPFALFET WLNEAIKSEP NDPNAMALAT VDPDGLPDVR 

        70         80         90        100        110        120 
MVLMKGFDTE GFVFYSHIAS QKGRELAANP KAALLFHWKS LRRQVRIRGN VTPVTDAEAD 

       130        140        150        160        170        180 
AYFATRPKQA QIGAWASKQS EALESRFAFE QAIAKVAAKY IIGEVPRPPG WSGWRITPVR 

       190        200        210 
IEFWHDRPFR LHDRIEFRRD AAGQKWSKTR MYP

« Hide

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References

[1]"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110."
Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.
DNA Res. 9:189-197(2002) [PubMed: 12597275] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: USDA 110.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ		BA000040 Genomic DNA. Translation: BAC47889.1.
RefSeqNP_769264.1.

3D structure databases

SMRQ89RY8. Positions 13-213.
ModBaseSearch...

Genome annotation databases

GeneID1051429.
GenomeReviewsGene locus bll2624 in contig BA000040_GR.
KEGGbja:bll2624.
NMPDRfig|224911.1.peg.2624.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG327559.
OMAHWSGFRI.
PhylomeDBQ89RY8.

Enzyme and pathway databases

BioCycBJAP224911:BLL2624-MONOMER.
BRENDA1.4.3.5. 280.

Family and domain databases

HAMAPMF_01629. PdxH.
[Tree]
InterProIPR000659. Pyridoxamine_oxidase.
IPR019740. Pyridoxamine_oxidase_CS.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR011576. PyridoxamineP_oxidase_FMN-bd.
IPR009002. Split_barrel_FMN-bd_related.
IPR012349. Split_barrel_FMN_bd.
[Graphical view]
Gene3DG3DSA:2.30.110.10. PNPOx_FMN_bd. 1 hit.
PANTHERPTHR10851. Pyridox_oxidase. 1 hit.
PfamPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
TIGRFAMsTIGR00558. pdxH. 1 hit.
PROSITEPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry namePDXH_BRAJA
AccessionPrimary (citable) accession number: Q89RY8
Entry history
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: June 1, 2003
Last modified: February 9, 2010
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents