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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Bacteroides fragilis (strain YCH46)
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 sitei83 – 831FMNUniRule annotation
Binding sitei86 – 861FMN; via amide nitrogenUniRule annotation
Binding sitei88 – 881SubstrateUniRule annotation
Binding sitei105 – 1051FMNUniRule annotation
Binding sitei145 – 1451SubstrateUniRule annotation
Binding sitei149 – 1491SubstrateUniRule annotation
Binding sitei153 – 1531SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi98 – 992FMNUniRule annotation
Nucleotide bindingi162 – 1632FMNUniRule 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

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:BF1453
OrganismiBacteroides fragilis (strain YCH46)
Taxonomic identifieri295405 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesBacteroidaceaeBacteroides
ProteomesiUP000002197 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000167681Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi295405.BF1453.

Structurei

3D structure databases

ProteinModelPortaliQ64WC2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni30 – 334Substrate bindingUniRule annotation
Regioni213 – 2153Substrate 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.

Q64WC2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTDHVSTHP DSPLHGNGIG SEAINLAAIR QEYTKGGLKE GDLPDNPLSL
60 70 80 90 100
FNRWLHEAID AQVDEPTAML VGTVSPEGQP STRTVLLKDL HDGKFIFYTN
110 120 130 140 150
YESRKGTHLA KNPYISLSFV WHALERQVHI EGIASKVPAG ESDTYFRQRP
160 170 180 190 200
YKSRIGARIS PQSRPLKSRM QLIRNFVAEA ARWVGREVER PAHWGGYAVT
210 220 230
PHRIEFWQGR ANRLHDRFLY SLQPDGSWQK ERLAP
Length:235
Mass (Da):26,673
Last modified:October 24, 2004 - v1
Checksum:i6C6C85CC8E160374
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006841 Genomic DNA. Translation: BAD48204.1.
RefSeqiYP_098738.1. NC_006347.1.

Genome annotation databases

EnsemblBacteriaiBAD48204; BAD48204; BF1453.
GeneIDi3082379.
KEGGibfr:BF1453.
PATRICi21048603. VBIBacFra17906_1419.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006841 Genomic DNA. Translation: BAD48204.1.
RefSeqiYP_098738.1. NC_006347.1.

3D structure databases

ProteinModelPortaliQ64WC2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi295405.BF1453.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD48204; BAD48204; BF1453.
GeneIDi3082379.
KEGGibfr:BF1453.
PATRICi21048603. VBIBacFra17906_1419.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

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. "Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation."
    Kuwahara T., Yamashita A., Hirakawa H., Nakayama H., Toh H., Okada N., Kuhara S., Hattori M., Hayashi T., Ohnishi Y.
    Proc. Natl. Acad. Sci. U.S.A. 101:14919-14924(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: YCH46.

Entry informationi

Entry nameiPDXH_BACFR
AccessioniPrimary (citable) accession number: Q64WC2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2006
Last sequence update: October 24, 2004
Last modified: March 31, 2015
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

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.