PDP_STAAW
ID PDP_STAAW Reviewed; 433 AA.
AC Q8NVF6;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 12-DEC-2006, sequence version 2.
DT 03-AUG-2022, entry version 107.
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=MW2060;
OS Staphylococcus aureus (strain MW2).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=196620;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MW2;
RX PubMed=12044378; DOI=10.1016/s0140-6736(02)08713-5;
RA Baba T., Takeuchi F., Kuroda M., Yuzawa H., Aoki K., Oguchi A., Nagai Y.,
RA Iwama N., Asano K., Naimi T., Kuroda H., Cui L., Yamamoto K., Hiramatsu K.;
RT "Genome and virulence determinants of high virulence community-acquired
RT MRSA.";
RL Lancet 359:1819-1827(2002).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB95925.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; BA000033; BAB95925.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_001242310.1; NC_003923.1.
DR AlphaFoldDB; Q8NVF6; -.
DR SMR; Q8NVF6; -.
DR EnsemblBacteria; BAB95925; BAB95925; BAB95925.
DR KEGG; sam:MW2060; -.
DR HOGENOM; CLU_025040_0_1_9; -.
DR Proteomes; UP000000418; Chromosome.
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_0000269538"
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; 46378 MW; 02418FD7A5BA45A1 CRC64;
MRMIDIIEKK RDGHTLTTEE INFFIDGYVK GDIPDYQASS LAMAIYFQDM NDDERAALTM
AMVNSGDMID LSDIKGVKVD KHSTGGVGDT TTLVLAPLVA AVDVPVAKMS GRGLGHTGGT
IDKLEAIDGF HVEIDEATFV KLVNENKVAV VGQSGNLTPA DKKLYALRDV TGTVNSIPLI
ASSIMSKKIA AGADAIVLDV KTGSGAFMKT LEDAEALAHA MVRIGNNVGR NTMAIISDMN
QPLGRAIGNA LELQEAIDTL KGQGPKDLTE LVLTLGSQMV VLANKAETLE EARALLIEAI
NSGAALEKFK TFIKNQGGDE TVIDHPERLP QAQYQIEYKA KKSGYVTELV SNDIGVASMM
LGAGRLTKED DIDLAVGIVL NKKIGDKVEE GESLLTIHSN RQDVDDVVKK LDSSITIADH
VVSPTLIHKI IIE
