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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica)
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 sitei97FMNUniRule annotation1
Binding sitei98FMNUniRule annotation1
Binding sitei120FMNUniRule annotation1
Binding sitei138SubstrateUniRule annotation1
Binding sitei142SubstrateUniRule annotation1
Binding sitei146SubstrateUniRule annotation1
Binding sitei200FMNUniRule annotation1
Binding sitei210FMNUniRule 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:ECA1935
OrganismiPectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica)
Taxonomic identifieri218491 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaePectobacterium
Proteomesi
  • UP000007966 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001677051 – 227Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST227

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi218491.ECA1935.

Structurei

3D structure databases

ProteinModelPortaliQ6D5V3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni23 – 26Substrate bindingUniRule annotation4
Regioni206 – 208Substrate bindingUniRule annotation3

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.
OrthoDBiPOG091H054N.

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.

Q6D5V3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQERSPSDG TPLIQPADIA DIRREYTRGG LRRGDLPANP LDLFERWLKQ
60 70 80 90 100
ACEAKLADPT AMSVATVDER GQPYQRIVLL KHYDEKGMVF YTNMGSRKAH
110 120 130 140 150
HLENNPRISL LFPWHVLERQ VMVLGRVEKL PALEVLKYFH SRPKDSQIGA
160 170 180 190 200
WVSKQSSRIS ARGVLESKFL ELKQKFQNGE VPLPSFWGGF RVVIDSVEFW
210 220
QGGEHRLHDR FFYQRQEENW QIDRLAP
Length:227
Mass (Da):26,398
Last modified:August 16, 2004 - v1
Checksum:iE39BF5D3EAA573D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950851 Genomic DNA. Translation: CAG74838.1.
RefSeqiWP_011093501.1. NC_004547.2.

Genome annotation databases

EnsemblBacteriaiCAG74838; CAG74838; ECA1935.
GeneIDi2882128.
KEGGieca:ECA1935.
PATRICi20479164. VBIPecAtr54885_1968.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950851 Genomic DNA. Translation: CAG74838.1.
RefSeqiWP_011093501.1. NC_004547.2.

3D structure databases

ProteinModelPortaliQ6D5V3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi218491.ECA1935.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAG74838; CAG74838; ECA1935.
GeneIDi2882128.
KEGGieca:ECA1935.
PATRICi20479164. VBIPecAtr54885_1968.

Phylogenomic databases

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
HOGENOMiHOG000242755.
KOiK00275.
OMAiPEHWGGY.
OrthoDBiPOG091H054N.

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_PECAS
AccessioniPrimary (citable) accession number: Q6D5V3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: August 16, 2004
Last modified: November 2, 2016
This is version 88 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

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.