UniProtKB - P0AFI7 (PDXH_ECOLI)
Protein
Pyridoxine/pyridoxamine 5'-phosphate oxidase
Gene
pdxH
Organism
Escherichia coli (strain K12)
Status
Functioni
Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).3 Publications
Miscellaneous
Can bind a second molecule of pyridoxamine 5'-phosphate at a non-catalytic site in a cleft at the protein surface.
Catalytic activityi
Cofactori
FMN6 PublicationsNote: Binds 1 FMN per subunit.6 Publications
Kineticsi
Kcat is 0.3 sec(-1) for oxidase activity with pyridoxine 5'-phosphate as substrate (at pH 7.6 and 37 degrees Celsius).1 Publication
- KM=0.3 µM for pyridoxamine 5'-phosphate1 Publication
- KM=2 µM for pyridoxine 5'-phosphate (at pH 7.6 and 37 degrees Celsius)2 Publications
- KM=105 µM for pyridoxamine 5'-phosphate (at pH 7.6 and 37 degrees Celsius)1 Publication
: pyridoxal 5'-phosphate salvage Pathwayi
This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.Proteins known to be involved in this subpathway in this organism are:
- Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH), Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
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.Proteins known to be involved in this subpathway in this organism are:
- Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH), Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 72 | Substrate1 Publication | 1 | |
Binding sitei | 88 | FMN3 Publications | 1 | |
Binding sitei | 89 | FMN3 Publications | 1 | |
Binding sitei | 111 | FMN2 Publications | 1 | |
Binding sitei | 129 | Substrate1 Publication | 1 | |
Binding sitei | 133 | Substrate1 Publication | 1 | |
Binding sitei | 137 | Substrate1 Publication | 1 | |
Binding sitei | 191 | FMN1 Publication | 1 | |
Binding sitei | 201 | FMN2 Publications | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 67 – 72 | FMN3 Publications | 6 | |
Nucleotide bindingi | 82 – 83 | FMN3 Publications | 2 | |
Nucleotide bindingi | 146 – 147 | FMN3 Publications | 2 |
GO - Molecular functioni
- FMN binding Source: EcoCyc
- oxidoreductase activity Source: EcoliWiki
- phosphate ion binding Source: CAFA
- protein homodimerization activity Source: CAFA
- pyridoxamine-phosphate oxidase activity Source: EcoCyc
- riboflavin binding Source: CAFA
GO - Biological processi
- 'de novo' pyridoxal 5'-phosphate biosynthetic process Source: EcoCyc
- pyridoxal phosphate biosynthetic process Source: GO_Central
- pyridoxine biosynthetic process Source: UniProtKB-KW
Keywordsi
Molecular function | Oxidoreductase |
Biological process | Pyridoxine biosynthesis |
Ligand | Flavoprotein, FMN |
Enzyme and pathway databases
BioCyci | EcoCyc:PDXH-MONOMER MetaCyc:PDXH-MONOMER |
BRENDAi | 1.4.3.5, 2026 |
UniPathwayi | UPA01068;UER00304 UPA01068;UER00305 |
Names & Taxonomyi
Protein namesi | Recommended name: Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.53 Publications)Alternative name(s): PNP/PMP oxidase Short name: PNPOx Pyridoxal 5'-phosphate synthase |
Gene namesi | Name:pdxH Ordered Locus Names:b1638, JW1630 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
Cytosol
- cytosol Source: EcoCyc
Other locations
- protein-containing complex Source: CAFA
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 14 | R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 14 | R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 17 | Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 49 | D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. 1 Publication | 1 | |
Mutagenesisi | 197 | R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. 1 Publication | 1 | |
Mutagenesisi | 197 | R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. 1 Publication | 1 | |
Mutagenesisi | 199 | H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 199 | H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. 1 Publication | 1 |
Chemistry databases
DrugBanki | DB03247, Flavin mononucleotide DB03345, Mercaptoethanol |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | Removed1 Publication | |||
ChainiPRO_0000167706 | 2 – 218 | Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST | 217 |
Proteomic databases
jPOSTi | P0AFI7 |
PaxDbi | P0AFI7 |
PRIDEi | P0AFI7 |
Interactioni
Subunit structurei
Homodimer.
6 PublicationsGO - Molecular functioni
- protein homodimerization activity Source: CAFA
Protein-protein interaction databases
BioGRIDi | 4263488, 16 interactors 851147, 1 interactor |
DIPi | DIP-48024N |
IntActi | P0AFI7, 13 interactors |
STRINGi | 511145.b1638 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0AFI7 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P0AFI7 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 14 – 17 | Substrate binding1 Publication | 4 | |
Regioni | 197 – 199 | Substrate binding1 Publication | 3 |
Sequence similaritiesi
Belongs to the pyridoxamine 5'-phosphate oxidase family.Curated
Phylogenomic databases
eggNOGi | COG0259, Bacteria |
InParanoidi | P0AFI7 |
PhylomeDBi | P0AFI7 |
Family and domain databases
Gene3Di | 2.30.110.10, 1 hit |
HAMAPi | MF_01629, PdxH, 1 hit |
InterProi | View protein in InterPro IPR000659, Pyridox_Oxase IPR019740, Pyridox_Oxase_CS IPR011576, Pyridox_Oxase_put IPR019576, Pyridoxamine_oxidase_dimer_C IPR012349, Split_barrel_FMN-bd |
PANTHERi | PTHR10851, PTHR10851, 1 hit |
Pfami | View protein in Pfam PF10590, PNP_phzG_C, 1 hit PF01243, Putative_PNPOx, 1 hit |
PIRSFi | PIRSF000190, Pyd_amn-ph_oxd, 1 hit |
TIGRFAMsi | TIGR00558, pdxH, 1 hit |
PROSITEi | View protein in PROSITE PS01064, PYRIDOX_OXIDASE, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P0AFI7-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP
60 70 80 90 100
TAMVVATVDE HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS
110 120 130 140 150
LLFPWHTLER QVMVIGKAER LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI
160 170 180 190 200
SARGILESKF LELKQKFQQG EVPLPSFWGG FRVSLEQIEF WQGGEHRLHD
210
RFLYQRENDA WKIDRLAP
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M92351 Genomic DNA Translation: AAA24709.1 U00096 Genomic DNA Translation: AAC74710.1 AP009048 Genomic DNA Translation: BAA15399.1 |
PIRi | B43261 |
RefSeqi | NP_416155.1, NC_000913.3 WP_001282319.1, NZ_STEB01000003.1 |
Genome annotation databases
EnsemblBacteriai | AAC74710; AAC74710; b1638 BAA15399; BAA15399; BAA15399 |
GeneIDi | 58462440 946806 |
KEGGi | ecj:JW1630 eco:b1638 |
PATRICi | fig|1411691.4.peg.622 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M92351 Genomic DNA Translation: AAA24709.1 U00096 Genomic DNA Translation: AAC74710.1 AP009048 Genomic DNA Translation: BAA15399.1 |
PIRi | B43261 |
RefSeqi | NP_416155.1, NC_000913.3 WP_001282319.1, NZ_STEB01000003.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1DNL | X-ray | 1.80 | A | 20-218 | [»] | |
1G76 | X-ray | 2.20 | A | 1-218 | [»] | |
1G77 | X-ray | 2.10 | A | 1-218 | [»] | |
1G78 | X-ray | 2.20 | A | 1-218 | [»] | |
1G79 | X-ray | 2.00 | A | 1-218 | [»] | |
1JNW | X-ray | 2.07 | A | 1-218 | [»] | |
1WV4 | X-ray | 2.60 | A/B | 1-218 | [»] | |
SMRi | P0AFI7 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4263488, 16 interactors 851147, 1 interactor |
DIPi | DIP-48024N |
IntActi | P0AFI7, 13 interactors |
STRINGi | 511145.b1638 |
Chemistry databases
DrugBanki | DB03247, Flavin mononucleotide DB03345, Mercaptoethanol |
Proteomic databases
jPOSTi | P0AFI7 |
PaxDbi | P0AFI7 |
PRIDEi | P0AFI7 |
Genome annotation databases
EnsemblBacteriai | AAC74710; AAC74710; b1638 BAA15399; BAA15399; BAA15399 |
GeneIDi | 58462440 946806 |
KEGGi | ecj:JW1630 eco:b1638 |
PATRICi | fig|1411691.4.peg.622 |
Organism-specific databases
EchoBASEi | EB1450 |
Phylogenomic databases
eggNOGi | COG0259, Bacteria |
InParanoidi | P0AFI7 |
PhylomeDBi | P0AFI7 |
Enzyme and pathway databases
UniPathwayi | UPA01068;UER00304 UPA01068;UER00305 |
BioCyci | EcoCyc:PDXH-MONOMER MetaCyc:PDXH-MONOMER |
BRENDAi | 1.4.3.5, 2026 |
Miscellaneous databases
EvolutionaryTracei | P0AFI7 |
PROi | PR:P0AFI7 |
Family and domain databases
Gene3Di | 2.30.110.10, 1 hit |
HAMAPi | MF_01629, PdxH, 1 hit |
InterProi | View protein in InterPro IPR000659, Pyridox_Oxase IPR019740, Pyridox_Oxase_CS IPR011576, Pyridox_Oxase_put IPR019576, Pyridoxamine_oxidase_dimer_C IPR012349, Split_barrel_FMN-bd |
PANTHERi | PTHR10851, PTHR10851, 1 hit |
Pfami | View protein in Pfam PF10590, PNP_phzG_C, 1 hit PF01243, Putative_PNPOx, 1 hit |
PIRSFi | PIRSF000190, Pyd_amn-ph_oxd, 1 hit |
TIGRFAMsi | TIGR00558, pdxH, 1 hit |
PROSITEi | View protein in PROSITE PS01064, PYRIDOX_OXIDASE, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | PDXH_ECOLI | |
Accessioni | P0AFI7Primary (citable) accession number: P0AFI7 Secondary accession number(s): P28225 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 20, 2005 |
Last sequence update: | January 23, 2007 | |
Last modified: | April 7, 2021 | |
This is version 130 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families