PDP_GEOSE
ID PDP_GEOSE Reviewed; 433 AA.
AC P77836;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Pyrimidine-nucleoside phosphorylase {ECO:0000303|PubMed:8782414};
DE Short=PYNP {ECO:0000303|PubMed:9817849};
DE Short=Py-NPase {ECO:0000303|PubMed:8782414};
DE EC=2.4.2.2 {ECO:0000269|PubMed:8782414};
GN Name=pdp; Synonyms=pyn;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=TH 6-2;
RX PubMed=8987664; DOI=10.1271/bbb.60.1655;
RA Okuyama K., Hamamoto T., Noguchi T., Midorikawa Y.;
RT "Molecular cloning and expression of the pyrimidine nucleoside
RT phosphorylase gene from Bacillus stearothermophilus TH 6-2.";
RL Biosci. Biotechnol. Biochem. 60:1655-1659(1996).
RN [2]
RP PROTEIN SEQUENCE OF 1-12, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, AND SUBUNIT.
RC STRAIN=TH 6-2;
RX PubMed=8782414; DOI=10.1271/bbb.60.1179;
RA Hamamoto T., Noguchi T., Midorikawa Y.;
RT "Purification and characterization of purine nucleoside phosphorylase and
RT pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-
RT 2.";
RL Biosci. Biotechnol. Biochem. 60:1179-1180(1996).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-432 IN COMPLEX WITH
RP PSEUDOURIDINE; PHOSPHATE AND POTASSIUM, AND COFACTOR.
RX PubMed=9817849; DOI=10.1016/s0969-2126(98)00145-2;
RA Pugmire M.J., Ealick S.E.;
RT "The crystal structure of pyrimidine nucleoside phosphorylase in a closed
RT conformation.";
RL Structure 6:1467-1479(1998).
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:0000269|PubMed:8782414}.
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:0000269|PubMed:8782414};
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:0000269|PubMed:8782414};
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:0000269|PubMed:8782414};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000269|PubMed:9817849};
CC Note=Binds 1 K(+) ion per subunit. {ECO:0000269|PubMed:9817849};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:8782414}.
CC -!- SIMILARITY: Belongs to the thymidine/pyrimidine-nucleoside
CC phosphorylase family. {ECO:0000305}.
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DR EMBL; D87961; BAA13512.1; -; Genomic_DNA.
DR EMBL; D87959; BAA20903.1; -; Genomic_DNA.
DR PIR; JT0875; JT0875.
DR PDB; 1BRW; X-ray; 2.10 A; A/B=1-432.
DR PDBsum; 1BRW; -.
DR AlphaFoldDB; P77836; -.
DR SMR; P77836; -.
DR DrugBank; DB03419; Uracil.
DR KEGG; ag:BAA13512; -.
DR BioCyc; MetaCyc:MON-17881; -.
DR BRENDA; 2.4.2.2; 623.
DR EvolutionaryTrace; P77836; -.
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; ISS:CAFA.
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; ISS:CAFA.
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; Direct protein sequencing; Glycosyltransferase;
KW Metal-binding; Potassium; Transferase.
FT CHAIN 1..433
FT /note="Pyrimidine-nucleoside phosphorylase"
FT /id="PRO_0000059083"
FT BINDING 81..83
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 88
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 90
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 92
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 108..110
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 120
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 168
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 187
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 243
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 246
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT BINDING 255
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:9817849,
FT ECO:0007744|PDB:1BRW"
FT HELIX 3..11
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 52..64
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 91..100
FT /evidence="ECO:0007829|PDB:1BRW"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 120..124
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 136..146
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 159..170
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 177..191
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 194..203
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 211..227
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 231..238
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 250..260
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 266..282
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 285..288
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 289..302
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 304..315
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 333..339
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 341..349
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 351..361
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 377..381
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 393..402
FT /evidence="ECO:0007829|PDB:1BRW"
FT HELIX 405..412
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 415..420
FT /evidence="ECO:0007829|PDB:1BRW"
FT STRAND 427..432
FT /evidence="ECO:0007829|PDB:1BRW"
SQ SEQUENCE 433 AA; 46332 MW; 75EF04B8E7B2E0AD CRC64;
MRMVDLIEKK RDGHALTKEE IQFIIEGYTK GDIPDYQMSA LAMAIFFRGM NEEETAELTM
AMVHSGDTID LSRIEGIKVD KHSTGGVGDT TTLVLGPLVA SVGVPVAKMS GRGLGHTGGT
IDKLESVPGF HVEITNDEFI DLVNKNKIAV VGQSGNLTPA DKKLYALRDV TATVNSIPLI
ASSIMSKKIA AGADAIVLDV KTGVGAFMKD LNDAKALAKA MVDIGNRVGR KTMAIISDMS
QPLGYAIGNA LEVKEAIDTL KGEGPEDFQE LCLVLGSHMV YLAEKASSLE EARHMLEKAM
KDGSALQTFK TFLAAQGGDA SVVDDPSKLP QAKYIIELEA KEDGYVSEIV ADAVGTAAMW
LGAGRATKES TIDLAVGLVL RKKVGDAVKK GESLVTIYSN REQVDDVKQK LYENIRISAT
PVQAPTLIYD KIS
