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P0AFI7 (PDXH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:pdxH
Ordered Locus Names:b1638, JW1630
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length218 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). HAMAP-Rule MF_01629

Catalytic activity

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. HAMAP-Rule MF_01629

Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. HAMAP-Rule MF_01629

Cofactor

Binds 1 FMN per subunit.

Pathway

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP-Rule MF_01629

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.

Subunit structure

Homodimer. Ref.7 Ref.8 Ref.9 Ref.10

Miscellaneous

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

Sequence similarities

Belongs to the pyridoxamine 5'-phosphate oxidase family.

Biophysicochemical properties

Kinetic parameters:

KM=0.3 µM for pyridoxamine 5'-phosphate Ref.9

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5
Chain2 – 218217Pyridoxine/pyridoxamine 5'-phosphate oxidase HAMAP-Rule MF_01629
PRO_0000167706

Regions

Nucleotide binding82 – 832FMN HAMAP-Rule MF_01629
Nucleotide binding146 – 1472FMN HAMAP-Rule MF_01629
Region14 – 174Substrate binding HAMAP-Rule MF_01629
Region197 – 1993Substrate binding HAMAP-Rule MF_01629

Sites

Binding site671FMN
Binding site701FMN; via amide nitrogen
Binding site721Substrate
Binding site891FMN
Binding site1291Substrate
Binding site1331Substrate
Binding site1371Substrate

Experimental info

Mutagenesis141R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. Ref.9
Mutagenesis141R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. Ref.9
Mutagenesis171Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. Ref.9
Mutagenesis491D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. Ref.9
Mutagenesis1971R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. Ref.9
Mutagenesis1971R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. Ref.9
Mutagenesis1991H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. Ref.9
Mutagenesis1991H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. Ref.9

Secondary structure

........................................ 218
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AFI7 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 8B47CEEEA6CEF5F9

FASTA21825,545
        10         20         30         40         50         60 
MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP TAMVVATVDE 

        70         80         90        100        110        120 
HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS LLFPWHTLER QVMVIGKAER 

       130        140        150        160        170        180 
LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI SARGILESKF LELKQKFQQG EVPLPSFWGG 

       190        200        210 
FRVSLEQIEF WQGGEHRLHD RFLYQRENDA WKIDRLAP 

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M92351 Genomic DNA. Translation: AAA24709.1.
U00096 Genomic DNA. Translation: AAC74710.1.
AP009048 Genomic DNA. Translation: BAA15399.1.
PIRB43261.
RefSeqNP_416155.1. NC_000913.3.
YP_489902.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
DisProtDP00165.
ProteinModelPortalP0AFI7.
SMRP0AFI7. Positions 5-218.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-48024N.
IntActP0AFI7. 13 interactions.
STRING511145.b1638.

Proteomic databases

PaxDbP0AFI7.
PRIDEP0AFI7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74710; AAC74710; b1638.
BAA15399; BAA15399; BAA15399.
GeneID12934494.
946806.
KEGGecj:Y75_p1615.
eco:b1638.
PATRIC32118578. VBIEscCol129921_1709.

Organism-specific databases

EchoBASEEB1450.
EcoGeneEG11487. pdxH.

Phylogenomic databases

eggNOGCOG0259.
HOGENOMHOG000242755.
KOK00275.
OMAPEHWGGY.
OrthoDBEOG60KN2Z.
PhylomeDBP0AFI7.
ProtClustDBPRK05679.

Enzyme and pathway databases

BioCycEcoCyc:PDXH-MONOMER.
ECOL316407:JW1630-MONOMER.
MetaCyc:PDXH-MONOMER.
UniPathwayUPA00190; UER00304.
UPA00190; UER00305.

Gene expression databases

GenevestigatorP0AFI7.

Family and domain databases

Gene3D2.30.110.10. 1 hit.
HAMAPMF_01629. PdxH.
InterProIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERPTHR10851. PTHR10851. 1 hit.
PfamPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMSSF50475. SSF50475. 1 hit.
TIGRFAMsTIGR00558. pdxH. 1 hit.
PROSITEPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0AFI7.
PROP0AFI7.

Entry information

Entry namePDXH_ECOLI
AccessionPrimary (citable) accession number: P0AFI7
Secondary accession number(s): P28225
Entry history
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 81 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene