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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Mycobacterium bovis (strain BCG / Tokyo 172 / ATCC 35737 / TMC 1019)
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: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei81SubstrateUniRule annotation1
Binding sitei98FMNUniRule annotation1
Binding sitei120FMNUniRule annotation1
Binding sitei138SubstrateUniRule annotation1
Binding sitei142SubstrateUniRule annotation1
Binding sitei201FMNUniRule annotation1
Binding sitei211FMNUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi76 – 81FMNUniRule annotation6
Nucleotide bindingi91 – 92FMNUniRule annotation2
Nucleotide bindingi155 – 156FMNUniRule annotation2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; 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:JTY_2626
OrganismiMycobacterium bovis (strain BCG / Tokyo 172 / ATCC 35737 / TMC 1019)
Taxonomic identifieri561275 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001863191 – 224Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST224

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliC1AF78.
SMRiC1AF78.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni19 – 22Substrate bindingUniRule annotation4
Regioni207 – 209Substrate bindingUniRule annotation3

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
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:SF0. PTHR10851:SF0. 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.

C1AF78-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDDDAQMVAI DKDQLARMRG EYGPEKDGCG DLDFDWLDDG WLTLLRRWLN
60 70 80 90 100
DAQRAGVSEP NAMVLATVAD GKPVTRSVLC KILDESGVAF FTSYTSAKGE
110 120 130 140 150
QLAVTPYASA TFPWYQLGRQ AHVQGPVSKV STEEIFTYWS MRPRGAQLGA
160 170 180 190 200
WASQQSRPVG SRAQLDNQLA EVTRRFADQD QIPVPPGWGG YRIAPEIVEF
210 220
WQGRENRMHN RIRVANGRLE RLQP
Length:224
Mass (Da):25,186
Last modified:May 26, 2009 - v1
Checksum:i66ABC0AAACE90DC1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP010918 Genomic DNA. Translation: BAH26907.1.

Genome annotation databases

EnsemblBacteriaiBAH26907; BAH26907; JTY_2626.
KEGGimbt:JTY_2626.
PATRICi18025005. VBIMycBov85238_2871.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP010918 Genomic DNA. Translation: BAH26907.1.

3D structure databases

ProteinModelPortaliC1AF78.
SMRiC1AF78.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH26907; BAH26907; JTY_2626.
KEGGimbt:JTY_2626.
PATRICi18025005. VBIMycBov85238_2871.

Phylogenomic databases

HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH. 1 hit.
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:SF0. PTHR10851:SF0. 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...

Entry informationi

Entry nameiPDXH_MYCBT
AccessioniPrimary (citable) accession number: C1AF78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: November 2, 2016
This is version 51 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.