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Q5DYB5

- PDXH_VIBF1

UniProt

Q5DYB5 - PDXH_VIBF1

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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Vibrio fischeri (strain ATCC 700601 / ES114)
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
Binding sitei130 – 1301SubstrateUniRule 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

BioCyciAFIS312309:GIWP-3920-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:VF_A1161
OrganismiVibrio fischeri (strain ATCC 700601 / ES114)
Taxonomic identifieri312309 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
ProteomesiUP000000537: Chromosome II

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 211211Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000167766Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi312309.VF_A1161.

Structurei

3D structure databases

ProteinModelPortaliQ5DYB5.
SMRiQ5DYB5. Positions 2-211.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni7 – 104Substrate bindingUniRule annotation
Regioni190 – 1923Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiNMGSRKA.
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.

Q5DYB5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MELEDIRRDY SLGGLRRADL PQEPVELFEL WLKQAVEAKL TDPTAMTVAT
60 70 80 90 100
VDENGQPFQR IVLLKHFDKT GFVFYTNLGS RKAQQLEQHS KISLHFPWHP
110 120 130 140 150
LERQVHITGT AEKLTALENM KYFTSRPKES QIAAWASKQS SRLTARAALE
160 170 180 190 200
GKYLELKQKF AKGEIPVPKF WGGFRIKIDS IEFWQGGDHR LHDRFLYSKD
210
QNDWQIDRLA P
Length:211
Mass (Da):24,524
Last modified:March 15, 2005 - v1
Checksum:i4C5CE5C7949B1410
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000021 Genomic DNA. Translation: AAW88231.1.
RefSeqiYP_207119.1. NC_006841.2.

Genome annotation databases

EnsemblBacteriaiAAW88231; AAW88231; VF_A1161.
GeneIDi3280611.
KEGGivfi:VF_A1161.
PATRICi20118319. VBIVibFis127983_3760.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000021 Genomic DNA. Translation: AAW88231.1 .
RefSeqi YP_207119.1. NC_006841.2.

3D structure databases

ProteinModelPortali Q5DYB5.
SMRi Q5DYB5. Positions 2-211.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 312309.VF_A1161.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAW88231 ; AAW88231 ; VF_A1161 .
GeneIDi 3280611.
KEGGi vfi:VF_A1161.
PATRICi 20118319. VBIVibFis127983_3760.

Phylogenomic databases

eggNOGi COG0259.
HOGENOMi HOG000242755.
KOi K00275.
OMAi NMGSRKA.
OrthoDBi EOG60KN2Z.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci AFIS312309:GIWP-3920-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: ATCC 700601 / ES114.

Entry informationi

Entry nameiPDXH_VIBF1
AccessioniPrimary (citable) accession number: Q5DYB5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 15, 2005
Last modified: October 1, 2014
This is version 67 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