PDP_STAEQ
ID PDP_STAEQ Reviewed; 433 AA.
AC Q5HM85;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=SERP1744;
OS Staphylococcus epidermidis (strain ATCC 35984 / RP62A).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=176279;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35984 / RP62A;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
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; CP000029; AAW55074.1; -; Genomic_DNA.
DR RefSeq; WP_002440546.1; NC_002976.3.
DR AlphaFoldDB; Q5HM85; -.
DR SMR; Q5HM85; -.
DR STRING; 176279.SERP1744; -.
DR EnsemblBacteria; AAW55074; AAW55074; SERP1744.
DR KEGG; ser:SERP1744; -.
DR eggNOG; COG0213; Bacteria.
DR HOGENOM; CLU_025040_0_1_9; -.
DR OMA; DVWRRMI; -.
DR OrthoDB; 1724909at2; -.
DR Proteomes; UP000000531; 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; Reference proteome;
KW Transferase.
FT CHAIN 1..433
FT /note="Pyrimidine-nucleoside phosphorylase"
FT /id="PRO_0000269539"
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; 46272 MW; DE572ED726936387 CRC64;
MRMIDIIEKK RDGKSLTKEE IEFFVNGYTH GEVPDYQASS LAMAIFFQDM NDEERAALTM
SMVNSGEKID LSDINGIKVD KHSTGGVGDT TTLVLAPLVA AVGVPVAKMS GRGLGHTGGT
IDKLESVKGF NVEISEKDFI KLVNDNQVAV IGQSGNLTPA DKKLYALRDV TGTVNSIPLI
ASSIMSKKIA AGADAIVLDV KTGSGAFMKT LDDAEALAHA MVRIGNNVGR NTMAIISDMS
QPLGNAIGNA LELKEAIATL KGNGPKDLTE LVLTLGSQMV VLAEQATSLD EARQMLIDAI
KTGKALNKFK TFLSNQGGDD SIVDSPEKLP SAKYQVEFKA KKDGYITEII ANEIGVASMM
LGAGRQTKED VIDLGVGIVL NKKVGEHVEK GENILTIHTN TKEIDDILYK LDNSITIESK
GEAPTLIHKI ITE
