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Q89RY8

- PDXH_BRADU

UniProt

Q89RY8 - PDXH_BRADU

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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed - 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

Binds 1 FMN per subunit.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei60 – 601FMNUniRule annotation
Binding sitei63 – 631FMN; via amide nitrogenUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Binding sitei82 – 821FMNUniRule annotation
Binding sitei122 – 1221SubstrateUniRule annotation
Binding sitei126 – 1261SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi75 – 762FMNUniRule annotation
Nucleotide bindingi139 – 1402FMNUniRule 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

BioCyciBJAP224911:GJEJ-2647-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:bll2624
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 213213Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000167692Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224911.bll2624.

Structurei

3D structure databases

ProteinModelPortaliQ89RY8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni190 – 1923Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
InParanoidiQ89RY8.
KOiK00275.
OrthoDBiEOG60KN2Z.
PhylomeDBiQ89RY8.

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.

Q89RY8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTDTTSMKHQ TPLTSGDFTA ADEPFALFET WLNEAIKSEP NDPNAMALAT
60 70 80 90 100
VDPDGLPDVR MVLMKGFDTE GFVFYSHIAS QKGRELAANP KAALLFHWKS
110 120 130 140 150
LRRQVRIRGN VTPVTDAEAD AYFATRPKQA QIGAWASKQS EALESRFAFE
160 170 180 190 200
QAIAKVAAKY IIGEVPRPPG WSGWRITPVR IEFWHDRPFR LHDRIEFRRD
210
AAGQKWSKTR MYP
Length:213
Mass (Da):24,181
Last modified:June 1, 2003 - v1
Checksum:iD12CF55C86CFBFB6
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000040 Genomic DNA. Translation: BAC47889.1.
RefSeqiNP_769264.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC47889; BAC47889; BAC47889.
GeneIDi1051429.
KEGGibja:bll2624.
PATRICi21188678. VBIBraJap65052_2598.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000040 Genomic DNA. Translation: BAC47889.1 .
RefSeqi NP_769264.1. NC_004463.1.

3D structure databases

ProteinModelPortali Q89RY8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224911.bll2624.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAC47889 ; BAC47889 ; BAC47889 .
GeneIDi 1051429.
KEGGi bja:bll2624.
PATRICi 21188678. VBIBraJap65052_2598.

Phylogenomic databases

eggNOGi COG0259.
HOGENOMi HOG000242755.
InParanoidi Q89RY8.
KOi K00275.
OrthoDBi EOG60KN2Z.
PhylomeDBi Q89RY8.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci BJAP224911:GJEJ-2647-MONOMER.

Family and domain databases

Gene3Di 2.30.110.10. 1 hit.
HAMAPi MF_01629. PdxH.
InterProi IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view ]
PANTHERi PTHR10851. PTHR10851. 1 hit.
Pfami PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view ]
PIRSFi PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMi SSF50475. SSF50475. 1 hit.
TIGRFAMsi TIGR00558. pdxH. 1 hit.
PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Entry informationi

Entry nameiPDXH_BRADU
AccessioniPrimary (citable) accession number: Q89RY8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: June 1, 2003
Last modified: October 29, 2014
This is version 78 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