PDX3_YEAST
ID PDX3_YEAST Reviewed; 228 AA.
AC P38075; D6VQ35;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 190.
DE RecName: Full=Pyridoxamine 5'-phosphate oxidase;
DE EC=1.4.3.5;
DE AltName: Full=PNP/PMP oxidase;
DE Short=PNPOx;
GN Name=PDX3; OrderedLocusNames=YBR035C; ORFNames=YBR0321;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7896706; DOI=10.1128/jb.177.7.1817-1823.1995;
RA Loubbardi A., Karst F., Guilloton M., Marcireau C.;
RT "Sterol uptake induced by an impairment of pyridoxal phosphate synthesis in
RT Saccharomyces cerevisiae: cloning and sequencing of the PDX3 gene encoding
RT pyridoxine (pyridoxamine) phosphate oxidase.";
RL J. Bacteriol. 177:1817-1823(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091864; DOI=10.1002/yea.320100010;
RA Smits P.H.M., de Haan M., Maat C., Grivell L.A.;
RT "The complete sequence of a 33 kb fragment on the right arm of chromosome
RT II from Saccharomyces cerevisiae reveals 16 open reading frames, including
RT ten new open reading frames, five previously identified genes and a
RT homologue of the SCO1 gene.";
RL Yeast 10:S75-S80(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [6]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-29, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=SUB592;
RX PubMed=12872131; DOI=10.1038/nbt849;
RA Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G.,
RA Roelofs J., Finley D., Gygi S.P.;
RT "A proteomics approach to understanding protein ubiquitination.";
RL Nat. Biotechnol. 21:921-926(2003).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=22984289; DOI=10.1074/mcp.m112.021105;
RA Voegtle F.N., Burkhart J.M., Rao S., Gerbeth C., Hinrichs J.,
RA Martinou J.C., Chacinska A., Sickmann A., Zahedi R.P., Meisinger C.;
RT "Intermembrane space proteome of yeast mitochondria.";
RL Mol. Cell. Proteomics 11:1840-1852(2012).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FMN.
RG New York structural genomix research consortium (NYSGXRC);
RT "The structure of PNP oxidase from S. cerevisiae.";
RL Submitted (JAN-2005) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the oxidation of either pyridoxine 5'-phosphate
CC (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate
CC (PLP).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) +
CC pyridoxal 5'-phosphate; Xref=Rhea:RHEA:15817, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58451, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:15149, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:58589, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Note=Binds 1 FMN per subunit.;
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space
CC {ECO:0000269|PubMed:22984289}.
CC -!- SIMILARITY: Belongs to the pyridoxamine 5'-phosphate oxidase family.
CC {ECO:0000305}.
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DR EMBL; X76078; CAA53690.1; -; Genomic_DNA.
DR EMBL; X76992; CAA54295.1; -; Genomic_DNA.
DR EMBL; Z35904; CAA84977.1; -; Genomic_DNA.
DR EMBL; AY557712; AAS56038.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07155.1; -; Genomic_DNA.
DR PIR; S41301; S41301.
DR RefSeq; NP_009591.1; NM_001178383.1.
DR PDB; 1CI0; X-ray; 2.70 A; A/B=1-228.
DR PDBsum; 1CI0; -.
DR AlphaFoldDB; P38075; -.
DR SMR; P38075; -.
DR BioGRID; 32736; 268.
DR DIP; DIP-4324N; -.
DR IntAct; P38075; 2.
DR STRING; 4932.YBR035C; -.
DR iPTMnet; P38075; -.
DR MaxQB; P38075; -.
DR PaxDb; P38075; -.
DR PRIDE; P38075; -.
DR EnsemblFungi; YBR035C_mRNA; YBR035C; YBR035C.
DR GeneID; 852323; -.
DR KEGG; sce:YBR035C; -.
DR SGD; S000000239; PDX3.
DR VEuPathDB; FungiDB:YBR035C; -.
DR eggNOG; KOG2586; Eukaryota.
DR GeneTree; ENSGT00390000011219; -.
DR HOGENOM; CLU_032263_2_0_1; -.
DR OMA; PEPNAMV; -.
DR BioCyc; MetaCyc:YBR035C-MON; -.
DR BioCyc; YEAST:YBR035C-MON; -.
DR Reactome; R-SCE-964975; Vitamins B6 activation to pyridoxal phosphate.
DR UniPathway; UPA01068; UER00304.
DR UniPathway; UPA01068; UER00305.
DR EvolutionaryTrace; P38075; -.
DR PRO; PR:P38075; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38075; protein.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0010181; F:FMN binding; IDA:SGD.
DR GO; GO:0004733; F:pyridoxamine-phosphate oxidase activity; IDA:SGD.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IC:SGD.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 2.30.110.10; -; 1.
DR HAMAP; MF_01629; PdxH; 1.
DR InterPro; IPR000659; Pyridox_Oxase.
DR InterPro; IPR019740; Pyridox_Oxase_CS.
DR InterPro; IPR011576; Pyridox_Oxase_put.
DR InterPro; IPR019576; Pyridoxamine_oxidase_dimer_C.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR PANTHER; PTHR10851; PTHR10851; 1.
DR Pfam; PF10590; PNP_phzG_C; 1.
DR Pfam; PF01243; Putative_PNPOx; 1.
DR PIRSF; PIRSF000190; Pyd_amn-ph_oxd; 1.
DR TIGRFAMs; TIGR00558; pdxH; 1.
DR PROSITE; PS01064; PYRIDOX_OXIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; Isopeptide bond; Mitochondrion;
KW Oxidoreductase; Pyridoxine biosynthesis; Reference proteome;
KW Ubl conjugation.
FT CHAIN 1..228
FT /note="Pyridoxamine 5'-phosphate oxidase"
FT /id="PRO_0000167787"
FT BINDING 20..23
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 73..76
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|Ref.8"
FT BINDING 78
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 88..89
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|Ref.8"
FT BINDING 95..96
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|Ref.8"
FT BINDING 118
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 136
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 140
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 144
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 153..154
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|Ref.8"
FT BINDING 199
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 205..207
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 209
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT CROSSLNK 29
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:12872131"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:1CI0"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 57..64
FT /evidence="ECO:0007829|PDB:1CI0"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 69..76
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:1CI0"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 105..112
FT /evidence="ECO:0007829|PDB:1CI0"
FT TURN 113..116
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 117..127
FT /evidence="ECO:0007829|PDB:1CI0"
FT HELIX 130..139
FT /evidence="ECO:0007829|PDB:1CI0"
FT HELIX 142..150
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:1CI0"
FT HELIX 160..173
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 186..200
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 208..213
FT /evidence="ECO:0007829|PDB:1CI0"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:1CI0"
SQ SEQUENCE 228 AA; 26908 MW; 8B648A219763160E CRC64;
MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP RETLPEAITF
SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI ATNPNAAIVF FWKDLQRQVR
VEGITEHVNR ETSERYFKTR PRGSKIGAWA SRQSDVIKNR EELDELTQKN TERFKDAEDI
PCPDYWGGLR IVPLEIEFWQ GRPSRLHDRF VYRRKTENDP WKVVRLAP
