DEOD3_SHEON
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 03-AUG-2022, entry version 103.
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}; OrderedLocusNames=SO_2719;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; 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; Q8EDM4; -.
DR KEGG; son:SO_2719; -.
DR PATRIC; fig|211586.12.peg.2619; -.
DR eggNOG; COG0813; Bacteria.
DR HOGENOM; CLU_068457_2_0_6; -.
DR OMA; MYYDPDE; -.
DR OrthoDB; 1028277at2; -.
DR PhylomeDB; Q8EDM4; -.
DR BioCyc; SONE211586:G1GMP-2501-MON; -.
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; -; 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 PANTHER; PTHR43691:SF2; PTHR43691:SF2; 1.
DR Pfam; PF01048; PNP_UDP_1; 1.
DR SUPFAM; SSF53167; SSF53167; 1.
DR TIGRFAMs; TIGR00107; deoD; 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
