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PDP_STAES
ID   PDP_STAES               Reviewed;         433 AA.
AC   Q8CNH8;
DT   12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   03-AUG-2022, entry version 112.
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=SE_1735;
OS   Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC   Staphylococcus.
OX   NCBI_TaxID=176280;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 12228 / FDA PCI 1200;
RX   PubMed=12950922; DOI=10.1046/j.1365-2958.2003.03671.x;
RA   Zhang Y.-Q., Ren S.-X., Li H.-L., Wang Y.-X., Fu G., Yang J., Qin Z.-Q.,
RA   Miao Y.-G., Wang W.-Y., Chen R.-S., Shen Y., Chen Z., Yuan Z.-H.,
RA   Zhao G.-P., Qu D., Danchin A., Wen Y.-M.;
RT   "Genome-based analysis of virulence genes in a non-biofilm-forming
RT   Staphylococcus epidermidis strain (ATCC 12228).";
RL   Mol. Microbiol. 49:1577-1593(2003).
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; AE015929; AAO05334.1; -; Genomic_DNA.
DR   RefSeq; NP_765290.1; NC_004461.1.
DR   RefSeq; WP_002485262.1; NZ_WBME01000041.1.
DR   AlphaFoldDB; Q8CNH8; -.
DR   SMR; Q8CNH8; -.
DR   STRING; 176280.SE_1735; -.
DR   EnsemblBacteria; AAO05334; AAO05334; SE_1735.
DR   GeneID; 50018166; -.
DR   KEGG; sep:SE_1735; -.
DR   PATRIC; fig|176280.10.peg.1695; -.
DR   eggNOG; COG0213; Bacteria.
DR   HOGENOM; CLU_025040_0_1_9; -.
DR   OMA; DVWRRMI; -.
DR   Proteomes; UP000001411; 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_0000269540"
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;  46360 MW;  17847C0D45B0416F CRC64;
     MRMIDIIEKK RDGKSLTKEE IEFFVNGYTH EEVPDYQASS LAMAIFFQDM NDEERAALTM
     SMVNSGEKID LSDINGIKVD KHSTGGVGDT TTLVLAPLVA AVGVPVAKMS GRGLGHTGGT
     IDKLESVKGF NVEISEKDFI KLVNDNQVAV IGQSGNLTPA DKKLYALRDV TGTVNSIPLI
     ASSIMSKKIA AGADAIVLDV KTGSGAFMKT LDDAEALAHA MVRIGNNVGR NTMAIISDMS
     QPLGNAIGNA LELKEAISTL KGNGPKDLTE LVLTLGSQMV VLAEQATSLD EARQMLIDAI
     KTGKALNKFK TFLSNQGGDD SIVDSPEKLP SAKYQVEFKA KKDGYITEII ANEIGVASMM
     LGAGRQTKED VIDLGVGIVL NKKVGEHVEK GENILTIHTN TKEIDDILYK LDNSITIESK
     GEAPTLIHKI ITE
 
 
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