DEOD3_ALIF1
ID DEOD3_ALIF1 Reviewed; 239 AA.
AC Q5DYV8;
DT 10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 91.
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=VF_A0968;
OS Aliivibrio fischeri (strain ATCC 700601 / ES114) (Vibrio fischeri).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Aliivibrio.
OX NCBI_TaxID=312309;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700601 / ES114;
RX PubMed=15703294; DOI=10.1073/pnas.0409900102;
RA Ruby E.G., Urbanowski M., Campbell J., Dunn A., Faini M., Gunsalus R.,
RA Lostroh P., Lupp C., McCann J., Millikan D., Schaefer A., Stabb E.,
RA Stevens A., Visick K., Whistler C., Greenberg E.P.;
RT "Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with
RT pathogenic congeners.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:3004-3009(2005).
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; CP000021; AAW88038.1; -; Genomic_DNA.
DR RefSeq; WP_005423543.1; NC_006841.2.
DR RefSeq; YP_206926.1; NC_006841.2.
DR PDB; 4LDN; X-ray; 1.48 A; A=1-239.
DR PDBsum; 4LDN; -.
DR AlphaFoldDB; Q5DYV8; -.
DR SMR; Q5DYV8; -.
DR STRING; 312309.VF_A0968; -.
DR EnsemblBacteria; AAW88038; AAW88038; VF_A0968.
DR GeneID; 64240362; -.
DR KEGG; vfi:VF_A0968; -.
DR PATRIC; fig|312309.11.peg.3569; -.
DR eggNOG; COG0813; Bacteria.
DR HOGENOM; CLU_068457_2_0_6; -.
DR OMA; FAMIADF; -.
DR OrthoDB; 1028277at2; -.
DR Proteomes; UP000000537; Chromosome II.
DR GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0009164; P:nucleoside catabolic process; IEA:UniProt.
DR GO; GO:0042278; P:purine nucleoside metabolic process; IEA:UniProtKB-UniRule.
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; IPR018016; Nucleoside_phosphorylase_CS.
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.
DR PROSITE; PS01232; PNP_UDP_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosyltransferase; Reference proteome; Transferase.
FT CHAIN 1..239
FT /note="Purine nucleoside phosphorylase DeoD-type"
FT /id="PRO_0000063173"
FT ACT_SITE 205
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT BINDING 5
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 21
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 25
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 44
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 88..91
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 180..182
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 204..205
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 218
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT STRAND 15..19
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 23..33
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 35..41
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 67..78
FT /evidence="ECO:0007829|PDB:4LDN"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 85..94
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 104..112
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:4LDN"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 132..143
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 166..173
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 183..193
FT /evidence="ECO:0007829|PDB:4LDN"
FT STRAND 196..206
FT /evidence="ECO:0007829|PDB:4LDN"
FT TURN 207..210
FT /evidence="ECO:0007829|PDB:4LDN"
FT HELIX 215..235
FT /evidence="ECO:0007829|PDB:4LDN"
SQ SEQUENCE 239 AA; 26542 MW; 0B35489AA6A19951 CRC64;
MSTPHINAPL DAFADTILMP GDPLRAKLIA ETYLENVVQV TDVRGMLGFT GEFKGRKISV
MGHGMGAPSA SIYFHELMTT YKVKNFIRIG SCGAIHDDVK LKDLIVAIGA STDSKMNRIR
FKDNDFAATA NYNMLSECVN TLKTTDINYL VGNVFSSDLF YRPDEEQYDM MARYGILGVE
MEVNALYSAA AENHCNAVAL CTVTDHIKNH EHLTADERRT ELHEMINVAL DVALKLPTE
