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UniProtKB/Swiss-Prot entry P38075


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name PDX3_YEAST
Primary accession number P38075
Secondary accession numbers None
Integrated into Swiss-Prot on October 1, 1994
Sequence was last modified on October 1, 1994 (Sequence version 1)
Annotations were last modified on    November 25, 2008 (Entry version 85)
Name and origin of the protein
Protein name Pyridoxamine 5'-phosphate oxidase
Synonyms EC 1.4.3.5
PNP/PMP oxidase
PNPOx
Gene name
Name: PDX3
OrderedLocusNames: YBR035C
ORFNames: YBR0321
From
Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932] 
Taxonomy Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=7896706 [NCBI, ExPASy, EBI, Israel, Japan]
Loubbardi A., Karst F., Guilloton M., Marcireau C.;
"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.";
J. Bacteriol. 177:1817-1823(1995).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
DOI=10.1002/yea.320100010; PubMed=8091864 [NCBI, ExPASy, EBI, Israel, Japan]
Smits P.H.M., de Haan M., Maat C., Grivell L.A.;
"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.";
Yeast 10:S75-S80(1994).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7813418 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Complete DNA sequence of yeast chromosome II.";
EMBO J. 13:5795-5809(1994).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
DOI=10.1101/gr.6037607; PubMed=17322287 [NCBI, ExPASy, EBI, Israel, Japan]
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., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-29, AND MASS SPECTROMETRY.
DOI=10.1038/nbt849; PubMed=12872131 [NCBI, ExPASy, EBI, Israel, Japan]
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.;
"A proteomics approach to understanding protein ubiquitination.";
Nat. Biotechnol. 21:921-926(2003).
[6]
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FMN.
New York structural genomix research consortium (NYSGXRC);
"The structure of PNP oxidase from S. cerevisiae.";
Submitted (JAN-2005) to the PDB data bank.
Comments
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
X76078; CAA53690.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
X76992; CAA54295.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z35904; CAA84977.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY557712; AAS56038.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR S41301; S41301.
RefSeq NP_009591.1; -.
3D structure databases
PDB
1CI0; X-ray; 2.70 A; A/B=1-228.[ExPASy / RCSB / EBI]
PDBsum 1CI0; -.
ModBase P38075.
Protein-protein interaction databases
DIP DIP:4324N; -.
IntAct P38075; -.
Organism-specific databases
CYGD YBR035c; -.
SGD S000000239; PDX3.
Yeast-GFP YBR035C.
Gene expression databases
GermOnline YBR035C; Saccharomyces cerevisiae.
Ontologies
GO
GO:0010181; Molecular function: FMN binding (inferred from electronic annotation from InterPro).
GO:0004733; Molecular function: pyridoxamine-phosphate oxidase activity (inferred from electronic annotation from InterPro).
GO:0006631; Biological process: fatty acid metabolic process (inferred from mutant phenotype from SGD).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
GO:0008615; Biological process: pyridoxine biosynthetic process (inferred from electronic annotation from InterPro).
QuickGo view.
Family and domain databases
InterPro IPR011576; PNPOx_rel_FMN_bd_core.
IPR000659; Pyridox_oxidase.
IPR012349; Split_barrel_FMN_bd.
Graphical view of domain structure.
Gene3D G3DSA:2.30.110.10; PNPOx_FMN_bd; 1.
PANTHER PTHR10851; Pyridox_oxidase; 1.
Pfam PF01243; Pyridox_oxidase; 1.
Pfam graphical view of domain structure.
ProDom PD006312; Pyridox_oxidase; 1.
[Domain structure / List of seq. sharing at least 1 domain]
TIGRFAMs TIGR00558; pdxH; 1.
PROSITE PS01064; PYRIDOX_OXIDASE; 1.
ProtoNet P38075.
Proteomic databases
PeptideAtlas P38075; -.
Genome annotation databases
Ensembl YBR035C; Saccharomyces cerevisiae. [Contig view]
GeneID 852323; -.
GenomeReviews Y13134_GR; YBR035C.
KEGG sce:YBR035C; -.
NMPDR fig|4932.3.peg.286; -.
Phylogenomic databases
HOGENOM P38075; -.
Other
LinkHub P38075; -.
NextBio 971023; -.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Complete proteome; Flavoprotein; FMN; Oxidoreductase; Pyridoxine biosynthesis; Ubl conjugation.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   228  228     Pyridoxamine 5'-phosphate oxidase. PRO_0000167787
NP_BIND   88    89  2     FMN. 
NP_BIND   153   154  2     FMN. 
REGION   205   207  3     Substrate binding (By similarity). 
BINDING   73    73        FMN. 
BINDING   76    76        FMN; via amide nitrogen. 
BINDING   78    78        Substrate (By similarity). 
BINDING   96    96        FMN. 
BINDING   136   136        Substrate (By similarity). 
BINDING   140   140        Substrate (By similarity). 
BINDING   144   144        Substrate (By similarity). 
CROSSLNK   29    29        Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin). 
HELIX   28    30  3      
HELIX   35    48  14      
STRAND   57    64  8      
TURN   65    68  4      
STRAND   69    76  8      
STRAND   82    90  9      
STRAND   92    94  3      
HELIX   95   102  8      
STRAND   105   112  8      
TURN   113   116  4      
STRAND   117   127  11      
HELIX   130   139  10      
HELIX   142   150  9      
STRAND   156   158  3      
HELIX   160   173  14      
STRAND   186   200  15      
STRAND   208   213  6      
STRAND   222   226  5      
Sequence information
Length: 228 AA [This is the length of the unprocessed precursor] Molecular weight: 26908 Da [This is the MW of the unprocessed precursor] CRC64: 8B648A219763160E [This is a checksum on the sequence]
        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 

P38075 in FASTA format

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