PDP_STAAB
ID PDP_STAAB Reviewed; 433 AA.
AC Q2YUL7;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=Pyrimidine-nucleoside phosphorylase;
DE Short=PYNP;
DE Short=Py-NPase;
DE EC=2.4.2.2;
GN Name=pdp; Synonyms=pyn; OrderedLocusNames=SAB2020c;
OS Staphylococcus aureus (strain bovine RF122 / ET3-1).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=273036;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=bovine RF122 / ET3-1;
RX PubMed=17971880; DOI=10.1371/journal.pone.0001120;
RA Herron-Olson L., Fitzgerald J.R., Musser J.M., Kapur V.;
RT "Molecular correlates of host specialization in Staphylococcus aureus.";
RL PLoS ONE 2:E1120-E1120(2007).
CC -!- FUNCTION: Catalyzes phosphorolysis of the pyrimidine nucleosides
CC uridine, thymidine and 2'-deoxyuridine with the formation of the
CC corresponding pyrimidine base and ribose-1-phosphate.
CC {ECO:0000250|UniProtKB:P77836}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + uridine = alpha-D-ribose 1-phosphate + uracil;
CC Xref=Rhea:RHEA:24388, ChEBI:CHEBI:16704, ChEBI:CHEBI:17568,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57720; EC=2.4.2.2;
CC Evidence={ECO:0000250|UniProtKB:P77836};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate +
CC thymine; Xref=Rhea:RHEA:16037, ChEBI:CHEBI:17748, ChEBI:CHEBI:17821,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57259; EC=2.4.2.2;
CC Evidence={ECO:0000250|UniProtKB:P77836};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxyuridine + phosphate = 2-deoxy-alpha-D-ribose 1-
CC phosphate + uracil; Xref=Rhea:RHEA:22824, ChEBI:CHEBI:16450,
CC ChEBI:CHEBI:17568, ChEBI:CHEBI:43474, ChEBI:CHEBI:57259; EC=2.4.2.2;
CC Evidence={ECO:0000250|UniProtKB:P77836};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000250|UniProtKB:P77836};
CC Note=Binds 1 K(+) ion per subunit. {ECO:0000250|UniProtKB:P77836};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P77836}.
CC -!- SIMILARITY: Belongs to the thymidine/pyrimidine-nucleoside
CC phosphorylase family. {ECO:0000305}.
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DR EMBL; AJ938182; CAI81709.1; -; Genomic_DNA.
DR RefSeq; WP_001242300.1; NC_007622.1.
DR AlphaFoldDB; Q2YUL7; -.
DR SMR; Q2YUL7; -.
DR KEGG; sab:SAB2020c; -.
DR HOGENOM; CLU_025040_0_1_9; -.
DR OMA; DVWRRMI; -.
DR GO; GO:0004645; F:1,4-alpha-oligoglucan phosphorylase activity; IEA:InterPro.
DR GO; GO:0047847; F:deoxyuridine phosphorylase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016154; F:pyrimidine-nucleoside phosphorylase activity; IEA:UniProtKB-EC.
DR GO; GO:0009032; F:thymidine phosphorylase activity; IEA:RHEA.
DR GO; GO:0004850; F:uridine phosphorylase activity; IEA:RHEA.
DR GO; GO:0006206; P:pyrimidine nucleobase metabolic process; IEA:InterPro.
DR GO; GO:0006213; P:pyrimidine nucleoside metabolic process; IEA:InterPro.
DR Gene3D; 3.40.1030.10; -; 1.
DR Gene3D; 3.90.1170.30; -; 1.
DR InterPro; IPR000312; Glycosyl_Trfase_fam3.
DR InterPro; IPR017459; Glycosyl_Trfase_fam3_N_dom.
DR InterPro; IPR036320; Glycosyl_Trfase_fam3_N_dom_sf.
DR InterPro; IPR035902; Nuc_phospho_transferase.
DR InterPro; IPR036566; PYNP-like_C_sf.
DR InterPro; IPR013102; PYNP_C.
DR InterPro; IPR018090; Pyrmidine_PPas_bac/euk.
DR InterPro; IPR017872; Pyrmidine_PPase_CS.
DR InterPro; IPR000053; Thymidine/pyrmidine_PPase.
DR PANTHER; PTHR10515; PTHR10515; 1.
DR Pfam; PF02885; Glycos_trans_3N; 1.
DR Pfam; PF00591; Glycos_transf_3; 1.
DR Pfam; PF07831; PYNP_C; 1.
DR PIRSF; PIRSF000478; TP_PyNP; 1.
DR SMART; SM00941; PYNP_C; 1.
DR SUPFAM; SSF47648; SSF47648; 1.
DR SUPFAM; SSF52418; SSF52418; 1.
DR SUPFAM; SSF54680; SSF54680; 1.
DR TIGRFAMs; TIGR02644; Y_phosphoryl; 1.
DR PROSITE; PS00647; THYMID_PHOSPHORYLASE; 1.
PE 3: Inferred from homology;
KW Glycosyltransferase; Metal-binding; Potassium; Transferase.
FT CHAIN 1..433
FT /note="Pyrimidine-nucleoside phosphorylase"
FT /id="PRO_0000269532"
FT BINDING 81..83
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 88
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 90
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 92
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 108..110
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 120
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 168
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 187
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 243
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 246
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P77836"
FT BINDING 255
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P77836"
SQ SEQUENCE 433 AA; 46367 MW; 02539190A3F94A14 CRC64;
MRMIDIIEKK RDGHTLTTEE INFFIDGYVK GDIPDYQASS LAMAIYFQDM NDDERAALTM
AMVNSGDMID LSDIKGVKVD KHSTGGVGDT TTLVLAPLVA AVDVPVAKMS GRGLGHTGGT
IDKLEAIDGF HVEIDEATFV KLVNENKVAV VGQSGNLTPA DKKIYALRDV TGTVNSIPLI
ASSIMSKKIA AGADAIVLDV KTGSGAFMKT LEDAEALAHA MVRIGNNVGR NTMAIISDMN
QPLGRAIGNA LELQEAIDTL KGQGPKDLTE LVLTLGSQMV VLANKAETLE EARALLIEAI
DSGAALEKFK TFIKNQGGDE TVIDHPERLP QAQYQIEYKA KKSGYVTELV SNDIGVASMM
LGAGRLTKED DIDLAVGIVL NKKIGDKVEE GESLLTIHSN RQDVDDVVKK LDSSITIADH
VVSPTLIHKI ITE
