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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Shewanella frigidimarina (strain NCIMB 400)
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 sitei61 – 611FMNUniRule annotation
Binding sitei64 – 641FMN; via amide nitrogenUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Binding sitei83 – 831FMNUniRule annotation
Binding sitei123 – 1231SubstrateUniRule annotation
Binding sitei127 – 1271SubstrateUniRule annotation
Binding sitei131 – 1311SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi76 – 772FMNUniRule annotation
Nucleotide bindingi140 – 1412FMNUniRule 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

BioCyciSFRI318167:GIXS-1767-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:Sfri_1702
OrganismiShewanella frigidimarina (strain NCIMB 400)
Taxonomic identifieri318167 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000000684: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 212212Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000292327Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi318167.Sfri_1702.

Structurei

3D structure databases

ProteinModelPortaliQ083L3.
SMRiQ083L3. Positions 1-212.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 114Substrate bindingUniRule annotation
Regioni191 – 1933Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
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.

Q083L3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDLSDIRRE YTQGGLRRAN LPVNPMDLFE QWMQQAKDAQ LSDPTAMCVA
60 70 80 90 100
TVDEDGQPFQ RIVLLKKFDD NGFVFFTNLE SRKAKQIATN SKISLLFPWH
110 120 130 140 150
PLERQVAVLG EAEPLSMLDV AKYFMSRPKD SQIAAWVSKQ SSKISARQAL
160 170 180 190 200
EGKFAEMKAK FAQGEVPLPK FWGGYLVRPA SIEFWQGGEH RLHDRFIYTK
210
TDADWNIDRL AP
Length:212
Mass (Da):24,242
Last modified:October 31, 2006 - v1
Checksum:i5155034EA1F276D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000447 Genomic DNA. Translation: ABI71552.1.
RefSeqiWP_011637168.1. NC_008345.1.
YP_750390.1. NC_008345.1.

Genome annotation databases

EnsemblBacteriaiABI71552; ABI71552; Sfri_1702.
GeneIDi4277727.
KEGGisfr:Sfri_1702.
PATRICi23497353. VBISheFri14343_1764.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000447 Genomic DNA. Translation: ABI71552.1.
RefSeqiWP_011637168.1. NC_008345.1.
YP_750390.1. NC_008345.1.

3D structure databases

ProteinModelPortaliQ083L3.
SMRiQ083L3. Positions 1-212.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi318167.Sfri_1702.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI71552; ABI71552; Sfri_1702.
GeneIDi4277727.
KEGGisfr:Sfri_1702.
PATRICi23497353. VBISheFri14343_1764.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciSFRI318167:GIXS-1767-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: NCIMB 400.

Entry informationi

Entry nameiPDXH_SHEFN
AccessioniPrimary (citable) accession number: Q083L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: October 31, 2006
Last modified: March 4, 2015
This is version 58 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.