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PDP_STAAM
ID   PDP_STAAM               Reviewed;         433 AA.
AC   Q99SC3;
DT   12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT   12-DEC-2006, sequence version 2.
DT   03-AUG-2022, entry version 122.
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=SAV2136;
OS   Staphylococcus aureus (strain Mu50 / ATCC 700699).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC   Staphylococcus.
OX   NCBI_TaxID=158878;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Mu50 / ATCC 700699;
RX   PubMed=11418146; DOI=10.1016/s0140-6736(00)04403-2;
RA   Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L.,
RA   Oguchi A., Aoki K., Nagai Y., Lian J.-Q., Ito T., Kanamori M.,
RA   Matsumaru H., Maruyama A., Murakami H., Hosoyama A., Mizutani-Ui Y.,
RA   Takahashi N.K., Sawano T., Inoue R., Kaito C., Sekimizu K., Hirakawa H.,
RA   Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K.,
RA   Furuya K., Yoshino C., Shiba T., Hattori M., Ogasawara N., Hayashi H.,
RA   Hiramatsu K.;
RT   "Whole genome sequencing of meticillin-resistant Staphylococcus aureus.";
RL   Lancet 357:1225-1240(2001).
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=BAB58298.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; BA000017; BAB58298.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_001242311.1; NC_002758.2.
DR   AlphaFoldDB; Q99SC3; -.
DR   SMR; Q99SC3; -.
DR   World-2DPAGE; 0002:Q99SC3; -.
DR   PaxDb; Q99SC3; -.
DR   EnsemblBacteria; BAB58298; BAB58298; SAV2136.
DR   KEGG; sav:SAV2136; -.
DR   HOGENOM; CLU_025040_0_1_9; -.
DR   OMA; DVWRRMI; -.
DR   PhylomeDB; Q99SC3; -.
DR   BioCyc; SAUR158878:SAV_RS11675-MON; -.
DR   Proteomes; UP000002481; 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_0000269534"
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;  46366 MW;  02507FD7A5BA45A1 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 ITE
 
 
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