PDP_BACSU
ID PDP_BACSU Reviewed; 433 AA.
AC P39142;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2003, sequence version 2.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Pyrimidine-nucleoside phosphorylase {ECO:0000303|PubMed:8550462};
DE Short=PYNP {ECO:0000250|UniProtKB:P77836};
DE Short=Py-NPase {ECO:0000250|UniProtKB:P77836};
DE EC=2.4.2.2 {ECO:0000269|PubMed:8550462};
GN Name=pdp {ECO:0000303|PubMed:8550462}; OrderedLocusNames=BSU39400;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP INDUCTION.
RC STRAIN=168;
RX PubMed=8550462; DOI=10.1128/jb.178.2.424-434.1996;
RA Saxild H.H., Andersen L.N., Hammer K.;
RT "Dra-nupC-pdp operon of Bacillus subtilis: nucleotide sequence, induction
RT by deoxyribonucleosides, and transcriptional regulation by the deoR-encoded
RT DeoR repressor protein.";
RL J. Bacteriol. 178:424-434(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / BGSC1A1;
RX PubMed=8867804; DOI=10.1093/dnares/2.6.295;
RA Yoshida K., Fujimyra M., Yanai N., Fujita Y.;
RT "Cloning and sequencing of a 23-kb region of the Bacillus subtilis genome
RT between the iol and hut operons.";
RL DNA Res. 2:295-301(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP SEQUENCE REVISION.
RX PubMed=10568751; DOI=10.1101/gr.9.11.1116;
RA Medigue C., Rose M., Viari A., Danchin A.;
RT "Detecting and analyzing DNA sequencing errors: toward a higher quality of
RT the Bacillus subtilis genome sequence.";
RL Genome Res. 9:1116-1127(1999).
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, ECO:0000269|PubMed:8550462}.
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:8550462};
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:8550462};
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 -!- INDUCTION: Induced by deoxyadenosine and thymidine. Repressed by DeoR
CC and glucose. {ECO:0000269|PubMed:8550462}.
CC -!- SIMILARITY: Belongs to the thymidine/pyrimidine-nucleoside
CC phosphorylase family. {ECO:0000305}.
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DR EMBL; X82174; CAA57664.1; -; Genomic_DNA.
DR EMBL; D45912; BAA08339.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15976.2; -; Genomic_DNA.
DR PIR; S78770; S49457.
DR RefSeq; NP_391819.2; NC_000964.3.
DR RefSeq; WP_003243952.1; NZ_JNCM01000034.1.
DR PDB; 5EP8; X-ray; 2.66 A; A/B=1-433.
DR PDB; 5OLN; X-ray; 1.88 A; A/B=1-433.
DR PDBsum; 5EP8; -.
DR PDBsum; 5OLN; -.
DR AlphaFoldDB; P39142; -.
DR SMR; P39142; -.
DR IntAct; P39142; 1.
DR STRING; 224308.BSU39400; -.
DR jPOST; P39142; -.
DR PaxDb; P39142; -.
DR PRIDE; P39142; -.
DR EnsemblBacteria; CAB15976; CAB15976; BSU_39400.
DR GeneID; 937540; -.
DR KEGG; bsu:BSU39400; -.
DR PATRIC; fig|224308.179.peg.4265; -.
DR eggNOG; COG0213; Bacteria.
DR InParanoid; P39142; -.
DR OMA; DVWRRMI; -.
DR PhylomeDB; P39142; -.
DR BioCyc; BSUB:BSU39400-MON; -.
DR BRENDA; 2.4.2.2; 658.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IBA:GO_Central.
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;
KW Reference proteome; Transferase.
FT CHAIN 1..433
FT /note="Pyrimidine-nucleoside phosphorylase"
FT /id="PRO_0000059084"
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 CONFLICT 88..96
FT /note="GDTTTLVLA -> WRHDNARSSS (in Ref. 1; CAA57664 and 2;
FT BAA08339)"
FT /evidence="ECO:0000305"
FT HELIX 2..11
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:5EP8"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 52..63
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 91..100
FT /evidence="ECO:0007829|PDB:5OLN"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 120..125
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 136..146
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 159..169
FT /evidence="ECO:0007829|PDB:5OLN"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 177..190
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 194..203
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 211..227
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 250..260
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 266..282
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 289..301
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 304..315
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 320..323
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 333..339
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 344..349
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 351..360
FT /evidence="ECO:0007829|PDB:5OLN"
FT TURN 361..363
FT /evidence="ECO:0007829|PDB:5EP8"
FT STRAND 364..367
FT /evidence="ECO:0007829|PDB:5EP8"
FT STRAND 377..381
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 392..402
FT /evidence="ECO:0007829|PDB:5OLN"
FT HELIX 405..413
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 415..419
FT /evidence="ECO:0007829|PDB:5OLN"
FT STRAND 426..431
FT /evidence="ECO:0007829|PDB:5OLN"
SQ SEQUENCE 433 AA; 46207 MW; 30C90542CE34206C CRC64;
MRMVDIIIKK QNGKELTTEE IQFFVNGYTD GSIPDYQASA LAMAIFFQDM SDRERADLTM
AMVNSGETID LSAIEGIKVD KHSTGGVGDT TTLVLAPLVA ALDVPVAKMS GRGLGHTGGT
IDKLEAIMGF HVELTKDEFI KLVNRDKVAV IGQSGNLTPA DKKLYALRDV TGTVNSIPLI
ASSIMSKKIA AGADAIVLDV KTGAGAFMKT EEDAAELAKA MVRIGNNVGR QTMAVISDMS
QPLGFAIGNA LEVKEAIDTL KGEGPEDLHE LVLTLGSQMV VLAKKADTLD EARAKLEEVM
KNGKALEKFK DFLKNQGGDS SIVDDPSKLP QAAYQIDVPA KEAGVVSEIV ADEIGVAAML
LGAGRATKED EIDLAVGIML RKKVGDKVEK GEPLVTLYAN RENVDEVIAK VYDNIRIAAE
AKAPKLIHTL ITE
