Reviewed,
UniProtKB/Swiss-Prot P38075 (PDX3_YEAST)
Last modified
June 16, 2009.
Version 90.
History...
Clusters with 100%,
90%,
50% identity |
Documents (5) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Pyridoxamine 5'-phosphate oxidase EC=1.4.3.5 Alternative name(s): PNP/PMP oxidase Short name=PNPOx | ||||||
| Gene names |
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| Organism | Saccharomyces cerevisiae (Baker's yeast) [Complete proteome] | ||||||
| Taxonomic identifier | 4932 [NCBI] | ||||||
| Taxonomic lineage | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces |
Protein attributes
| Sequence length | 228 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence 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). |
| Catalytic activity | Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. |
| Cofactor | Binds 1 FMN per subunit. |
| Pathway | |
| Subunit structure | Homodimer By similarity. |
| Sequence similarities | Belongs to the pyridoxamine 5'-phosphate oxidase family. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Pyridoxine biosynthesis |
| Ligand | FMN Flavoprotein |
| Molecular function | Oxidoreductase |
| PTM | Isopeptide bond Ubl conjugation |
| Technical term | 3D-structure Complete proteome |
| Gene Ontology (GO) | |
| Biological process | fatty acid metabolic process Ref.1 Inferred from mutant phenotype. Source: SGD oxidation reductionInferred from electronic annotation. Source: UniProtKB-KW pyridoxine biosynthetic processInferred from electronic annotation. Source: UniProtKB-KW |
| Molecular function | FMN binding Inferred from electronic annotation. Source: InterPro pyridoxamine-phosphate oxidase activity Ref.1Inferred from mutant phenotype. Source: SGD |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | |||||||||||||||||||||||||||||||||||
Molecule processing | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 228 | 228 | Pyridoxamine 5'-phosphate oxidase | PRO_0000167787 | ||||||||||||||||||||||||||||||||||||
Regions | ||||||||||||||||||||||||||||||||||||||||
| Nucleotide binding | 88 – 89 | 2 | FMN | |||||||||||||||||||||||||||||||||||||
| Nucleotide binding | 153 – 154 | 2 | FMN | |||||||||||||||||||||||||||||||||||||
| Region | 205 – 207 | 3 | Substrate binding By similarity | |||||||||||||||||||||||||||||||||||||
Sites | ||||||||||||||||||||||||||||||||||||||||
| Binding site | 73 | 1 | FMN | |||||||||||||||||||||||||||||||||||||
| Binding site | 76 | 1 | FMN; via amide nitrogen | |||||||||||||||||||||||||||||||||||||
| Binding site | 78 | 1 | Substrate By similarity | |||||||||||||||||||||||||||||||||||||
| Binding site | 96 | 1 | FMN | |||||||||||||||||||||||||||||||||||||
| Binding site | 136 | 1 | Substrate By similarity | |||||||||||||||||||||||||||||||||||||
| Binding site | 140 | 1 | Substrate By similarity | |||||||||||||||||||||||||||||||||||||
| Binding site | 144 | 1 | Substrate By similarity | |||||||||||||||||||||||||||||||||||||
Amino acid modifications | ||||||||||||||||||||||||||||||||||||||||
| Cross-link | 29 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.5 | ||||||||||||||||||||||||||||||||||||||
Secondary structure | ||||||||||||||||||||||||||||||||||||||||
Helix Strand Turn | ||||||||||||||||||||||||||||||||||||||||
| Helix | 28 – 30 | 3 | ||||||||||||||||||||||||||||||||||||||
| Helix | 35 – 48 | 14 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 57 – 64 | 8 | ||||||||||||||||||||||||||||||||||||||
| Turn | 65 – 68 | 4 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 69 – 76 | 8 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 82 – 90 | 9 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 92 – 94 | 3 | ||||||||||||||||||||||||||||||||||||||
| Helix | 95 – 102 | 8 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 105 – 112 | 8 | ||||||||||||||||||||||||||||||||||||||
| Turn | 113 – 116 | 4 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 117 – 127 | 11 | ||||||||||||||||||||||||||||||||||||||
| Helix | 130 – 139 | 10 | ||||||||||||||||||||||||||||||||||||||
| Helix | 142 – 150 | 9 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 156 – 158 | 3 | ||||||||||||||||||||||||||||||||||||||
| Helix | 160 – 173 | 14 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 186 – 200 | 15 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 208 – 213 | 6 | ||||||||||||||||||||||||||||||||||||||
| Beta strand | 222 – 226 | 5 | ||||||||||||||||||||||||||||||||||||||
Sequences
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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: 7896706] [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: 8091864] [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. Kleine K.EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c. |
| [4] | "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. LaBaer J.Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c. |
| [5] | "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: 12872131] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-29, MASS SPECTROMETRY. |
| [6] | "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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| X76078 Genomic DNA. Translation: CAA53690.1. X76992 Genomic DNA. Translation: CAA54295.1. Z35904 Genomic DNA. Translation: CAA84977.1. AY557712 Genomic DNA. Translation: AAS56038.1. | |||||||||||||
| PIR | S41301. | ||||||||||||
| RefSeq | NP_009591.1. | ||||||||||||
3D structure databases | |||||||||||||
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| ModBase | Search... | ||||||||||||
Protein-protein interaction databases | |||||||||||||
| DIP | DIP:4324N. | ||||||||||||
| IntAct | P38075. 3 interactions. | ||||||||||||
Proteomic databases | |||||||||||||
| PeptideAtlas | P38075. | ||||||||||||
| PRIDE | P38075. | ||||||||||||
Genome annotation databases | |||||||||||||
| Ensembl | YBR035C. Saccharomyces cerevisiae. [Contig view] | ||||||||||||
| GeneID | 852323. | ||||||||||||
| GenomeReviews | Gene locus YBR035C in contig Y13134_GR. | ||||||||||||
| KEGG | sce:YBR035C. | ||||||||||||
| NMPDR | fig|4932.3.peg.286. | ||||||||||||
Organism-specific databases | |||||||||||||
| CYGD | YBR035c. | ||||||||||||
| SGD | S000000239. PDX3. | ||||||||||||
| Yeast-GFP | Search... | ||||||||||||
Phylogenomic databases | |||||||||||||
| HOGENOM | P38075. | ||||||||||||
| OMA | P38075. FTFFTNY. | ||||||||||||
Enzyme and pathway databases | |||||||||||||
| BRENDA | 1.4.3.5. 250. | ||||||||||||
Gene expression databases | |||||||||||||
| GermOnline | YBR035C. Saccharomyces cerevisiae. | ||||||||||||
Family and domain databases | |||||||||||||
| InterPro | IPR011576. PNPOx_rel_FMN_bd_core. IPR000659. Pyridoxamine_oxidase. IPR019740. Pyridoxamine_oxidase_CS. IPR019576. Pyridoxamine_oxidase_dimer_C. IPR012349. Split_barrel_FMN_bd. [Graphical view] | ||||||||||||
| Gene3D | G3DSA:2.30.110.10. PNPOx_FMN_bd. 1 hit. | ||||||||||||
| PANTHER | PTHR10851. Pyridox_oxidase. 1 hit. | ||||||||||||
| Pfam | PF10590. PNPOx_C. 1 hit. PF01243. Pyridox_oxidase. 1 hit. [Graphical view] | ||||||||||||
| ProDom | PD006312. Pyridox_oxidase. 1 hit. [Graphical view] [Entries sharing at least one domain] | ||||||||||||
| TIGRFAMs | TIGR00558. pdxH. 1 hit. | ||||||||||||
| PROSITE | PS01064. PYRIDOX_OXIDASE. 1 hit. [Graphical view] | ||||||||||||
| ProtoNet | Search... | ||||||||||||
Other Resources | |||||||||||||
| NextBio | 971023. | ||||||||||||
Entry information
| Entry name | PDX3_YEAST | ||||||||
| Accession | Primary (citable) accession number: P38075 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | FPAP (Fungal Proteome Annotation Project) | ||||||||
Relevant documents
| PATHWAY comments Index of metabolic and biosynthesis pathways |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |
| Yeast Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD |
| Yeast chromosome II Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names |

Clusters with


