ID   DEOD3_SHEON             Reviewed;         234 AA.
AC   Q8EDM4;
DT   10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   27-MAR-2024, entry version 109.
DE   RecName: Full=Purine nucleoside phosphorylase DeoD-type {ECO:0000255|HAMAP-Rule:MF_01627};
DE            Short=PNP {ECO:0000255|HAMAP-Rule:MF_01627};
DE            EC=2.4.2.1 {ECO:0000255|HAMAP-Rule:MF_01627};
GN   Name=deoD3 {ECO:0000255|HAMAP-Rule:MF_01627};
GN   OrderedLocusNames=SO_2719;
OS   Shewanella oneidensis (strain MR-1).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=211586;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=MR-1;
RX   PubMed=12368813; DOI=10.1038/nbt749;
RA   Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA   Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA   Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA   DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA   Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA   Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA   Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA   Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT   "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT   Shewanella oneidensis.";
RL   Nat. Biotechnol. 20:1118-1123(2002).
CC   -!- FUNCTION: Catalyzes the reversible phosphorolytic breakdown of the N-
CC       glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the
CC       formation of the corresponding free purine bases and pentose-1-
CC       phosphate. {ECO:0000255|HAMAP-Rule:MF_01627}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a purine D-ribonucleoside + phosphate = a purine nucleobase +
CC         alpha-D-ribose 1-phosphate; Xref=Rhea:RHEA:19805, ChEBI:CHEBI:26386,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:57720, ChEBI:CHEBI:142355; EC=2.4.2.1;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01627};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-
CC         alpha-D-ribose 1-phosphate + a purine nucleobase;
CC         Xref=Rhea:RHEA:36431, ChEBI:CHEBI:26386, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:57259, ChEBI:CHEBI:142361; EC=2.4.2.1;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01627};
CC   -!- SUBUNIT: Homohexamer; trimer of homodimers. {ECO:0000255|HAMAP-
CC       Rule:MF_01627}.
CC   -!- SIMILARITY: Belongs to the PNP/UDP phosphorylase family.
CC       {ECO:0000255|HAMAP-Rule:MF_01627}.
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DR   EMBL; AE014299; AAN55747.1; -; Genomic_DNA.
DR   RefSeq; NP_718303.1; NC_004347.2.
DR   RefSeq; WP_011072663.1; NZ_CP053946.1.
DR   PDB; 4LKR; X-ray; 2.40 A; A=1-234.
DR   PDBsum; 4LKR; -.
DR   AlphaFoldDB; Q8EDM4; -.
DR   SMR; Q8EDM4; -.
DR   STRING; 211586.SO_2719; -.
DR   PaxDb; 211586-SO_2719; -.
DR   KEGG; son:SO_2719; -.
DR   PATRIC; fig|211586.12.peg.2619; -.
DR   eggNOG; COG0813; Bacteria.
DR   HOGENOM; CLU_068457_2_0_6; -.
DR   OrthoDB; 9782889at2; -.
DR   PhylomeDB; Q8EDM4; -.
DR   BioCyc; SONE211586:G1GMP-2501-MONOMER; -.
DR   Proteomes; UP000008186; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IBA:GO_Central.
DR   GO; GO:0006152; P:purine nucleoside catabolic process; IBA:GO_Central.
DR   CDD; cd09006; PNP_EcPNPI-like; 1.
DR   Gene3D; 3.40.50.1580; Nucleoside phosphorylase domain; 1.
DR   HAMAP; MF_01627; Pur_nucleosid_phosp; 1.
DR   InterPro; IPR004402; DeoD-type.
DR   InterPro; IPR000845; Nucleoside_phosphorylase_d.
DR   InterPro; IPR035994; Nucleoside_phosphorylase_sf.
DR   NCBIfam; TIGR00107; deoD; 1.
DR   PANTHER; PTHR43691:SF11; FI09636P-RELATED; 1.
DR   PANTHER; PTHR43691; URIDINE PHOSPHORYLASE; 1.
DR   Pfam; PF01048; PNP_UDP_1; 1.
DR   SUPFAM; SSF53167; Purine and uridine phosphorylases; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Glycosyltransferase; Reference proteome; Transferase.
FT   CHAIN           1..234
FT                   /note="Purine nucleoside phosphorylase DeoD-type"
FT                   /id="PRO_0000063161"
FT   ACT_SITE        204
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT   BINDING         4
FT                   /ligand="a purine D-ribonucleoside"
FT                   /ligand_id="ChEBI:CHEBI:142355"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         20
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /note="in other chain"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         24
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /note="in other chain"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         43
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         87..90
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /note="in other chain"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         179..181
FT                   /ligand="a purine D-ribonucleoside"
FT                   /ligand_id="ChEBI:CHEBI:142355"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /note="in other chain"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   BINDING         203..204
FT                   /ligand="a purine D-ribonucleoside"
FT                   /ligand_id="ChEBI:CHEBI:142355"
FT                   /ligand_note="ligand shared between dimeric partners"
FT                   /note="in other chain"
FT                   /evidence="ECO:0000250|UniProtKB:P50389"
FT   SITE            217
FT                   /note="Important for catalytic activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT   STRAND          14..18
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           22..31
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          34..40
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           42..44
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          47..52
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          55..60
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           66..79
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          84..93
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          103..112
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           115..119
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   TURN            120..122
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           131..143
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          148..155
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           166..172
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          177..181
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           182..192
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   STRAND          195..205
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   TURN            206..208
FT                   /evidence="ECO:0007829|PDB:4LKR"
FT   HELIX           214..232
FT                   /evidence="ECO:0007829|PDB:4LKR"
SQ   SEQUENCE   234 AA;  25529 MW;  666F9D55C6001908 CRC64;
     MTAHINAQPT DFAETVIMPG DPLRAKYIAE TYLTDAVEVT NVRNMLGYTG YYQGQRISVM
     GHGMGISSMV LYGHELINFF GVKRIIRIGS LGATQQHVEM RDVILAQAAG TDSPTNAKRS
     SGYHMATSAT FSLLHKAYTK ANEKGISVKV GNVFSGDLYY DPDEDMIPAL ERFGVLGIDM
     EVAGLYGLAH QQGIESLAIL TVSDHCLTGE ETTAQERQLS FNNMIELALE TALN
//