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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.

Cofactori

FMNNote: Binds 1 FMN per subunit.

Kineticsi

  1. KM=0.3 µM for pyridoxamine 5'-phosphate1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei67 – 671FMN3 Publications
Binding sitei70 – 701FMN; via amide nitrogen3 Publications
Binding sitei72 – 721Substrate
Binding sitei89 – 891FMN3 Publications
Binding sitei129 – 1291Substrate
Binding sitei133 – 1331Substrate
Binding sitei137 – 1371Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi82 – 832FMN3 Publications
Nucleotide bindingi146 – 1472FMN3 Publications

GO - Molecular functioni

  1. FMN binding Source: EcoCyc
  2. oxidoreductase activity Source: EcoliWiki
  3. pyridoxamine-phosphate oxidase activity Source: EcoCyc

GO - Biological processi

  1. oxidation-reduction process Source: EcoliWiki
  2. pyridoxal 5'-phosphate salvage Source: EcoCyc
  3. pyridoxine biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciEcoCyc:PDXH-MONOMER.
ECOL316407:JW1630-MONOMER.
MetaCyc:PDXH-MONOMER.
BRENDAi1.4.3.5. 2026.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Gene namesi
Name:pdxH
Ordered Locus Names:b1638, JW1630
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11487. pdxH.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi14 – 141R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. 1 Publication
Mutagenesisi14 – 141R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. 1 Publication
Mutagenesisi17 – 171Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. 1 Publication
Mutagenesisi49 – 491D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. 1 Publication
Mutagenesisi197 – 1971R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. 1 Publication
Mutagenesisi197 – 1971R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. 1 Publication
Mutagenesisi199 – 1991H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. 1 Publication
Mutagenesisi199 – 1991H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 218217Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000167706Add
BLAST

Proteomic databases

PaxDbiP0AFI7.
PRIDEiP0AFI7.

Expressioni

Gene expression databases

GenevestigatoriP0AFI7.

Interactioni

Subunit structurei

Homodimer.4 Publications

Protein-protein interaction databases

DIPiDIP-48024N.
IntActiP0AFI7. 13 interactions.
STRINGi511145.b1638.

Structurei

Secondary structure

1
218
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 124Combined sources
Helixi24 – 263Combined sources
Helixi31 – 4414Combined sources
Beta strandi52 – 587Combined sources
Beta strandi64 – 707Combined sources
Beta strandi73 – 753Combined sources
Beta strandi78 – 847Combined sources
Helixi88 – 958Combined sources
Beta strandi98 – 1036Combined sources
Helixi106 – 1083Combined sources
Beta strandi110 – 12011Combined sources
Helixi123 – 1308Combined sources
Helixi135 – 1439Combined sources
Helixi154 – 16613Combined sources
Beta strandi167 – 1704Combined sources
Beta strandi178 – 1836Combined sources
Beta strandi186 – 1927Combined sources
Helixi195 – 1973Combined sources
Beta strandi200 – 2067Combined sources
Beta strandi208 – 2158Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DNLX-ray1.80A20-218[»]
1G76X-ray2.20A1-218[»]
1G77X-ray2.10A1-218[»]
1G78X-ray2.20A1-218[»]
1G79X-ray2.00A1-218[»]
1JNWX-ray2.07A1-218[»]
1WV4X-ray2.60A/B1-218[»]
DisProtiDP00165.
ProteinModelPortaliP0AFI7.
SMRiP0AFI7. Positions 5-218.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFI7.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 174Substrate binding
Regioni197 – 1993Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
InParanoidiP0AFI7.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.
PhylomeDBiP0AFI7.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AFI7-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:218
Mass (Da):25,545
Last modified:January 22, 2007 - v2
Checksum:i8B47CEEEA6CEF5F9
GO

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.
PIRiB43261.
RefSeqiNP_416155.1. NC_000913.3.
YP_489902.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74710; AAC74710; b1638.
BAA15399; BAA15399; BAA15399.
GeneIDi12934494.
946806.
KEGGiecj:Y75_p1615.
eco:b1638.
PATRICi32118578. VBIEscCol129921_1709.

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.
PIRiB43261.
RefSeqiNP_416155.1. NC_000913.3.
YP_489902.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DNLX-ray1.80A20-218[»]
1G76X-ray2.20A1-218[»]
1G77X-ray2.10A1-218[»]
1G78X-ray2.20A1-218[»]
1G79X-ray2.00A1-218[»]
1JNWX-ray2.07A1-218[»]
1WV4X-ray2.60A/B1-218[»]
DisProtiDP00165.
ProteinModelPortaliP0AFI7.
SMRiP0AFI7. Positions 5-218.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48024N.
IntActiP0AFI7. 13 interactions.
STRINGi511145.b1638.

Proteomic databases

PaxDbiP0AFI7.
PRIDEiP0AFI7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74710; AAC74710; b1638.
BAA15399; BAA15399; BAA15399.
GeneIDi12934494.
946806.
KEGGiecj:Y75_p1615.
eco:b1638.
PATRICi32118578. VBIEscCol129921_1709.

Organism-specific databases

EchoBASEiEB1450.
EcoGeneiEG11487. pdxH.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
InParanoidiP0AFI7.
KOiK00275.
OMAiPHWGGFR.
OrthoDBiEOG60KN2Z.
PhylomeDBiP0AFI7.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciEcoCyc:PDXH-MONOMER.
ECOL316407:JW1630-MONOMER.
MetaCyc:PDXH-MONOMER.
BRENDAi1.4.3.5. 2026.

Miscellaneous databases

EvolutionaryTraceiP0AFI7.
PROiP0AFI7.

Gene expression databases

GenevestigatoriP0AFI7.

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

« Hide 'large scale' publications
  1. "Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations."
    Lam H.-M., Winkler M.E.
    J. Bacteriol. 174:6033-6045(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12."
    Zhao G., Winkler M.E.
    J. Bacteriol. 177:883-891(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION.
    Strain: K12.
  6. "Expression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase."
    di Salvo M., Yang E., Zhao G., Winkler M.E., Schirch V.
    Protein Expr. Purif. 13:349-356(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8-A resolution."
    Safo M.K., Mathews I., Musayev F.N., di Salvo M.L., Thiel D.J., Abraham D.J., Schirch V.
    Structure 8:751-762(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 20-218 IN COMPLEX WITH FMN, SUBUNIT.
  8. "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution."
    Safo M.K., Musayev F.N., di Salvo M.L., Schirch V.
    J. Mol. Biol. 310:817-826(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.
  9. "Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase."
    di Salvo M.L., Ko T.-P., Musayev F.N., Raboni S., Schirch V., Safo M.K.
    J. Mol. Biol. 315:385-397(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-14; TYR-17; ASP-49; ARG-197 AND HIS-199.
  10. "Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme."
    Safo M.K., Musayev F.N., Schirch V.
    Acta Crystallogr. D 61:599-604(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.

Entry informationi

Entry nameiPDXH_ECOLI
AccessioniPrimary (citable) accession number: P0AFI7
Secondary accession number(s): P28225
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 19, 2005
Last sequence update: January 22, 2007
Last modified: March 31, 2015
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Can bind a second molecule of pyridoxamine 5'-phosphate at a non-catalytic site in a cleft at the protein surface.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.