Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Alteromonas mediterranea (strain DSM 17117 / CIP 110805 / LMG 28347 / Deep ecotype)
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei65 – 651SubstrateUniRule annotation
Binding sitei81 – 811FMNUniRule annotation
Binding sitei82 – 821FMNUniRule annotation
Binding sitei104 – 1041FMNUniRule annotation
Binding sitei122 – 1221SubstrateUniRule annotation
Binding sitei126 – 1261SubstrateUniRule annotation
Binding sitei130 – 1301SubstrateUniRule annotation
Binding sitei184 – 1841FMNUniRule annotation
Binding sitei194 – 1941FMNUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi60 – 656FMNUniRule annotation
Nucleotide bindingi75 – 762FMNUniRule annotation
Nucleotide bindingi139 – 1402FMNUniRule annotation

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

BioCyciAMAC314275:GHA7-1043-MONOMER.
AMAC314275:GHA7-2525-MONOMER.
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:MADE_1012505Imported
ORF Names:MADE_1005140
OrganismiAlteromonas mediterranea (strain DSM 17117 / CIP 110805 / LMG 28347 / Deep ecotype)
Taxonomic identifieri1774373 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesAlteromonadaceaeAlteromonas
Proteomesi
  • UP000001870 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 212212Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_1000186288Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi314275.MADE_1005140.

Structurei

3D structure databases

ProteinModelPortaliB4RVA4.
SMRiB4RVA4. Positions 13-212.
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

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
KOiK00275.
OMAiPEHWGGY.

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: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.

B4RVA4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAISDMRRQY SKGSLSESDI TSSPFSLFDQ WLKDAIDAGI PDPTAMTVAT
60 70 80 90 100
VDSTGQPSQR IVLLKDVSDK GFVFFTNLGS RKAQELSVNP KVSCHFPWFF
110 120 130 140 150
MERQVRVCGS VEKLSVSENA AYFFSRPKDS QLAAYASKQS KPIGSRALLL
160 170 180 190 200
TQFKQLKDKF ANKALPVPDF WGGFRIVPHQ IEFWQGGEDR LHDRLEYNKA
210
EDGRWSTQRL MP
Length:212
Mass (Da):24,006
Last modified:September 23, 2008 - v1
Checksum:i351847BF9615C46B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001103 Genomic DNA. Translation: AEA98637.2.
RefSeqiWP_012517528.1. NC_011138.3.

Genome annotation databases

EnsemblBacteriaiAEA98637; AEA98637; MADE_1012505.
GeneIDi10557845.
KEGGiamc:MADE_1012505.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001103 Genomic DNA. Translation: AEA98637.2.
RefSeqiWP_012517528.1. NC_011138.3.

3D structure databases

ProteinModelPortaliB4RVA4.
SMRiB4RVA4. Positions 13-212.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi314275.MADE_1005140.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEA98637; AEA98637; MADE_1012505.
GeneIDi10557845.
KEGGiamc:MADE_1012505.

Phylogenomic databases

eggNOGiENOG4108S7T. Bacteria.
COG0259. LUCA.
KOiK00275.
OMAiPEHWGGY.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.
BioCyciAMAC314275:GHA7-1043-MONOMER.
AMAC314275:GHA7-2525-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: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...

Publicationsi

  1. "Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter."
    Ivars-Martinez E., Martin-Cuadrado A.-B., D'Auria G., Mira A., Ferriera S., Johnson J., Friedman R., Rodriguez-Valera F.
    ISME J. 2:1194-1212(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 17117 / CIP 110805 / LMG 28347 / Deep ecotype.

Entry informationi

Entry nameiPDXH_ALTMD
AccessioniPrimary (citable) accession number: B4RVA4
Secondary accession number(s): F2G240, F2G703
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: September 23, 2008
Last modified: June 8, 2016
This is version 60 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

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.