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Q89RY8

- PDXH_BRADU

UniProt

Q89RY8 - PDXH_BRADU

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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene
pdxH, bll2624
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) By similarity.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 By similarity.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei60 – 601FMN By similarity
Binding sitei63 – 631FMN; via amide nitrogen By similarity
Binding sitei65 – 651Substrate By similarity
Binding sitei82 – 821FMN By similarity
Binding sitei122 – 1221Substrate By similarity
Binding sitei126 – 1261Substrate By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi75 – 762FMN By similarity
Nucleotide bindingi139 – 1402FMN By similarity

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 oxidase (EC:1.4.3.5)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Gene namesi
Name:pdxH
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 oxidaseUniRule annotationPRO_0000167692Add
BLAST

Interactioni

Subunit structurei

Homodimer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi224911.bll2624.

Structurei

3D structure databases

ProteinModelPortaliQ89RY8.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni190 – 1923Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
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

MTDTTSMKHQ TPLTSGDFTA ADEPFALFET WLNEAIKSEP NDPNAMALAT    50
VDPDGLPDVR MVLMKGFDTE GFVFYSHIAS QKGRELAANP KAALLFHWKS 100
LRRQVRIRGN VTPVTDAEAD AYFATRPKQA QIGAWASKQS EALESRFAFE 150
QAIAKVAAKY IIGEVPRPPG WSGWRITPVR IEFWHDRPFR LHDRIEFRRD 200
AAGQKWSKTR MYP 213
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.
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: July 9, 2014
This is version 76 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

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