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P38075 (PDX3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 131. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | 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:
Pyridoxamine 5'-phosphate oxidase

EC=1.4.3.5
Alternative name(s):
PNP/PMP oxidase
Short name=PNPOx
Gene names
Name:PDX3
Ordered Locus Names:YBR035C
ORF Names:YBR0321
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length228 AA.
Sequence statusComplete.
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 By similarity. HAMAP-Rule MF_01629

Sequence similarities

Belongs to the pyridoxamine 5'-phosphate oxidase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 228228Pyridoxamine 5'-phosphate oxidase HAMAP-Rule MF_01629
PRO_0000167787

Regions

Nucleotide binding88 – 892FMN HAMAP-Rule MF_01629
Nucleotide binding153 – 1542FMN HAMAP-Rule MF_01629
Region205 – 2073Substrate binding By similarity

Sites

Binding site731FMN
Binding site761FMN; via amide nitrogen
Binding site781Substrate By similarity
Binding site961FMN
Binding site1361Substrate By similarity
Binding site1401Substrate By similarity
Binding site1441Substrate By similarity

Amino acid modifications

Cross-link29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.6

Secondary structure

................................ 228
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38075 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 8B648A219763160E

FASTA22826,908
        10         20         30         40         50         60 
MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP RETLPEAITF 

        70         80         90        100        110        120 
SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI ATNPNAAIVF FWKDLQRQVR 

       130        140        150        160        170        180 
VEGITEHVNR ETSERYFKTR PRGSKIGAWA SRQSDVIKNR EELDELTQKN TERFKDAEDI 

       190        200        210        220 
PCPDYWGGLR IVPLEIEFWQ GRPSRLHDRF VYRRKTENDP WKVVRLAP 

« Hide

References

« Hide 'large scale' references
[1]"Sterol uptake induced by an impairment of pyridoxal phosphate synthesis in Saccharomyces cerevisiae: cloning and sequencing of the PDX3 gene encoding pyridoxine (pyridoxamine) phosphate oxidase."
Loubbardi A., Karst F., Guilloton M., Marcireau C.
J. Bacteriol. 177:1817-1823(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene."
Smits P.H.M., de Haan M., Maat C., Grivell L.A.
Yeast 10:S75-S80(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"Complete DNA sequence of yeast chromosome II."
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. expand/collapse author list , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"A proteomics approach to understanding protein ubiquitination."
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.
Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-29.
Strain: SUB592.
[7]"The structure of PNP oxidase from S. cerevisiae."
New York structural genomix research consortium (NYSGXRC)
Submitted (JAN-2005) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FMN.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X76078 Genomic DNA. Translation: CAA53690.1.
X76992 Genomic DNA. Translation: CAA54295.1.
Z35904 Genomic DNA. Translation: CAA84977.1.
AY557712 Genomic DNA. Translation: AAS56038.1.
BK006936 Genomic DNA. Translation: DAA07155.1.
PIRS41301.
RefSeqNP_009591.1. NM_001178383.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CI0X-ray2.70A/B1-228[»]
ProteinModelPortalP38075.
SMRP38075. Positions 24-228.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32736. 107 interactions.
DIPDIP-4324N.
IntActP38075. 1 interaction.
MINTMINT-528829.
STRING4932.YBR035C.

Proteomic databases

PaxDbP38075.
PeptideAtlasP38075.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBR035C; YBR035C; YBR035C.
GeneID852323.
KEGGsce:YBR035C.

Organism-specific databases

CYGDYBR035c.
SGDS000000239. PDX3.

Phylogenomic databases

eggNOGCOG0259.
GeneTreeENSGT00390000011219.
HOGENOMHOG000242755.
KOK00275.
OMAPEHWGGY.
OrthoDBEOG7WDNF3.

Enzyme and pathway databases

BioCycMetaCyc:YBR035C-MONOMER.
YEAST:YBR035C-MONOMER.
UniPathwayUPA00190; UER00304.
UPA00190; UER00305.

Gene expression databases

GenevestigatorP38075.

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

EvolutionaryTraceP38075.
NextBio971023.
PROP38075.

Entry information

Entry namePDX3_YEAST
AccessionPrimary (citable) accession number: P38075
Secondary accession number(s): D6VQ35
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: March 19, 2014
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

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