PDP_STAAC
ID PDP_STAAC Reviewed; 433 AA.
AC Q5HE64;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-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=SACOL2128;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
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; CP000046; AAW38438.1; -; Genomic_DNA.
DR RefSeq; WP_001242318.1; NC_002951.2.
DR PDB; 3H5Q; X-ray; 1.94 A; A=1-433.
DR PDBsum; 3H5Q; -.
DR AlphaFoldDB; Q5HE64; -.
DR SMR; Q5HE64; -.
DR EnsemblBacteria; AAW38438; AAW38438; SACOL2128.
DR KEGG; sac:SACOL2128; -.
DR HOGENOM; CLU_025040_0_1_9; -.
DR OMA; DVWRRMI; -.
DR EvolutionaryTrace; Q5HE64; -.
DR Proteomes; UP000000530; 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 1: Evidence at protein level;
KW 3D-structure; Glycosyltransferase; Metal-binding; Potassium; Transferase.
FT CHAIN 1..433
FT /note="Pyrimidine-nucleoside phosphorylase"
FT /id="PRO_0000269533"
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"
FT HELIX 1..11
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 52..63
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 91..101
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 106..109
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 120..124
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 136..146
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 159..169
FT /evidence="ECO:0007829|PDB:3H5Q"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 177..190
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 194..203
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 211..228
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 250..260
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 266..282
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 289..301
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 304..315
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 321..324
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 333..339
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 344..349
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 351..360
FT /evidence="ECO:0007829|PDB:3H5Q"
FT TURN 361..363
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 377..381
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 392..402
FT /evidence="ECO:0007829|PDB:3H5Q"
FT HELIX 405..414
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 415..419
FT /evidence="ECO:0007829|PDB:3H5Q"
FT STRAND 426..431
FT /evidence="ECO:0007829|PDB:3H5Q"
SQ SEQUENCE 433 AA; 46308 MW; FC7FE95BB6477441 CRC64;
MRMIDIIEKK RDGHTLTTEE INFFIGGYVK 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
