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P0AFI7

- PDXH_ECOLI

UniProt

P0AFI7 - PDXH_ECOLI

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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene
pdxH, b1638, JW1630
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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).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

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 – 671FMN
Binding sitei70 – 701FMN; via amide nitrogen
Binding sitei72 – 721Substrate
Binding sitei89 – 891FMN
Binding sitei129 – 1291Substrate
Binding sitei133 – 1331Substrate
Binding sitei137 – 1371Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi82 – 832FMNUniRule annotation
Nucleotide bindingi146 – 1472FMNUniRule annotation

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.
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: Chromosome, UP000000625: 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 oxidaseUniRule annotationPRO_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 – 124
Helixi24 – 263
Helixi31 – 4414
Beta strandi52 – 587
Beta strandi64 – 707
Beta strandi73 – 753
Beta strandi78 – 847
Helixi88 – 958
Beta strandi98 – 1036
Helixi106 – 1083
Beta strandi110 – 12011
Helixi123 – 1308
Helixi135 – 1439
Helixi154 – 16613
Beta strandi167 – 1704
Beta strandi178 – 1836
Beta strandi186 – 1927
Helixi195 – 1973
Beta strandi200 – 2067
Beta strandi208 – 2158

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP0AFI7.

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiNMGSRKA.
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

MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP    50
TAMVVATVDE HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS 100
LLFPWHTLER QVMVIGKAER LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI 150
SARGILESKF LELKQKFQQG EVPLPSFWGG FRVSLEQIEF WQGGEHRLHD 200
RFLYQRENDA WKIDRLAP 218
Length:218
Mass (Da):25,545
Last modified:January 23, 2007 - v2
Checksum:i8B47CEEEA6CEF5F9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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.
YP_489902.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
DisProti DP00165.
ProteinModelPortali P0AFI7.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-48024N.
IntActi P0AFI7. 13 interactions.
STRINGi 511145.b1638.

Proteomic databases

PaxDbi P0AFI7.
PRIDEi P0AFI7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74710 ; AAC74710 ; b1638 .
BAA15399 ; BAA15399 ; BAA15399 .
GeneIDi 12934494.
946806.
KEGGi ecj:Y75_p1615.
eco:b1638.
PATRICi 32118578. VBIEscCol129921_1709.

Organism-specific databases

EchoBASEi EB1450.
EcoGenei EG11487. pdxH.

Phylogenomic databases

eggNOGi COG0259.
HOGENOMi HOG000242755.
KOi K00275.
OMAi NMGSRKA.
OrthoDBi EOG60KN2Z.
PhylomeDBi P0AFI7.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci EcoCyc:PDXH-MONOMER.
ECOL316407:JW1630-MONOMER.
MetaCyc:PDXH-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0AFI7.
PROi P0AFI7.

Gene expression databases

Genevestigatori P0AFI7.

Family and domain databases

Gene3Di 2.30.110.10. 1 hit.
HAMAPi MF_01629. PdxH.
InterProi IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view ]
PANTHERi PTHR10851. PTHR10851. 1 hit.
Pfami PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view ]
PIRSFi PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMi SSF50475. SSF50475. 1 hit.
TIGRFAMsi TIGR00558. pdxH. 1 hit.
PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

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(1992) [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(2006) [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(1995) [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(1998) [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(2000) [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(2001) [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(2002) [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(2005) [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 20, 2005
Last sequence update: January 23, 2007
Last modified: June 11, 2014
This is version 83 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

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