Pyridoxamine 5'-phosphate oxidase - Saccharomyces cerevisiae (Baker's yeast)

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

Name:	PDX3
Ordered Locus Names:	YBR035C
ORF Names:	YBR0321

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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	Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the pyridoxamine 5'-phosphate oxidase family.

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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 reduction Inferred from electronic annotation. Source: UniProtKB-KW pyridoxine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	FMN binding Inferred from electronic annotation. Source: InterPro pyridoxamine-phosphate oxidase activity Ref.1 Inferred from mutant phenotype. Source: SGD
Complete GO annotation...

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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

1

.

228

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P38075-1 [UniParc].

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

228

26,908

        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

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References

	« Hide 'large scale' referencesShow '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.

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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

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CI0	X-ray	2.70	A/B	1-228	[»]

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.

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Entry information

Entry name

PDX3_YEAST

Accession

Primary (citable) accession number: P38075

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	June 16, 2009
This is version 90 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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