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P38075

- PDX3_YEAST

UniProt

P38075 - PDX3_YEAST

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Protein

Pyridoxamine 5'-phosphate oxidase

Gene

PDX3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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).

Catalytic activityi

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

Cofactori

Binds 1 FMN per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei73 – 731FMN1 Publication
Binding sitei76 – 761FMN; via amide nitrogen1 Publication
Binding sitei78 – 781SubstrateBy similarity
Binding sitei96 – 961FMN1 Publication
Binding sitei136 – 1361SubstrateBy similarity
Binding sitei140 – 1401SubstrateBy similarity
Binding sitei144 – 1441SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi88 – 892FMN1 Publication
Nucleotide bindingi153 – 1542FMN1 Publication

GO - Molecular functioni

  1. FMN binding Source: InterPro
  2. pyridoxamine-phosphate oxidase activity Source: SGD

GO - Biological processi

  1. pyridoxal 5'-phosphate salvage Source: SGD
  2. pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciMetaCyc:YBR035C-MONOMER.
YEAST:YBR035C-MONOMER.
ReactomeiREACT_189056. Vitamins B6 activation to pyridoxal phosphate.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Gene namesi
Name:PDX3
Ordered Locus Names:YBR035C
ORF Names:YBR0321
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome II

Organism-specific databases

CYGDiYBR035c.
SGDiS000000239. PDX3.

Subcellular locationi

GO - Cellular componenti

  1. mitochondrial intermembrane space Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 228228Pyridoxamine 5'-phosphate oxidasePRO_0000167787Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP38075.
PaxDbiP38075.
PeptideAtlasiP38075.

Expressioni

Gene expression databases

GenevestigatoriP38075.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi32736. 108 interactions.
DIPiDIP-4324N.
IntActiP38075. 1 interaction.
MINTiMINT-528829.
STRINGi4932.YBR035C.

Structurei

Secondary structure

1
228
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi28 – 303
Helixi35 – 4814
Beta strandi57 – 648
Turni65 – 684
Beta strandi69 – 768
Beta strandi82 – 909
Beta strandi92 – 943
Helixi95 – 1028
Beta strandi105 – 1128
Turni113 – 1164
Beta strandi117 – 12711
Helixi130 – 13910
Helixi142 – 1509
Beta strandi156 – 1583
Helixi160 – 17314
Beta strandi186 – 20015
Beta strandi208 – 2136
Beta strandi222 – 2265

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CI0X-ray2.70A/B1-228[»]
ProteinModelPortaliP38075.
SMRiP38075. Positions 24-228.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38075.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni205 – 2073Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
GeneTreeiENSGT00390000011219.
HOGENOMiHOG000242755.
KOiK00275.
OMAiELDHRGF.
OrthoDBiEOG7WDNF3.

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.

P38075-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP
60 70 80 90 100
RETLPEAITF SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI
110 120 130 140 150
ATNPNAAIVF FWKDLQRQVR VEGITEHVNR ETSERYFKTR PRGSKIGAWA
160 170 180 190 200
SRQSDVIKNR EELDELTQKN TERFKDAEDI PCPDYWGGLR IVPLEIEFWQ
210 220
GRPSRLHDRF VYRRKTENDP WKVVRLAP
Length:228
Mass (Da):26,908
Last modified:October 1, 1994 - v1
Checksum:i8B648A219763160E
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS41301.
RefSeqiNP_009591.1. NM_001178383.1.

Genome annotation databases

EnsemblFungiiYBR035C; YBR035C; YBR035C.
GeneIDi852323.
KEGGisce:YBR035C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi S41301.
RefSeqi NP_009591.1. NM_001178383.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CI0 X-ray 2.70 A/B 1-228 [» ]
ProteinModelPortali P38075.
SMRi P38075. Positions 24-228.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32736. 108 interactions.
DIPi DIP-4324N.
IntActi P38075. 1 interaction.
MINTi MINT-528829.
STRINGi 4932.YBR035C.

Proteomic databases

MaxQBi P38075.
PaxDbi P38075.
PeptideAtlasi P38075.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YBR035C ; YBR035C ; YBR035C .
GeneIDi 852323.
KEGGi sce:YBR035C.

Organism-specific databases

CYGDi YBR035c.
SGDi S000000239. PDX3.

Phylogenomic databases

eggNOGi COG0259.
GeneTreei ENSGT00390000011219.
HOGENOMi HOG000242755.
KOi K00275.
OMAi ELDHRGF.
OrthoDBi EOG7WDNF3.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci MetaCyc:YBR035C-MONOMER.
YEAST:YBR035C-MONOMER.
Reactomei REACT_189056. Vitamins B6 activation to pyridoxal phosphate.

Miscellaneous databases

EvolutionaryTracei P38075.
NextBioi 971023.
PROi P38075.

Gene expression databases

Genevestigatori P38075.

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. "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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. 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.

Entry informationi

Entry nameiPDX3_YEAST
AccessioniPrimary (citable) accession number: P38075
Secondary accession number(s): D6VQ35
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: October 29, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3