DEOD_HELPY
ID DEOD_HELPY Reviewed; 233 AA.
AC P56463;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 1.
DT 03-AUG-2022, entry version 117.
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=deoD {ECO:0000255|HAMAP-Rule:MF_01627}; OrderedLocusNames=HP_1178;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
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; AE000511; AAD08222.1; -; Genomic_DNA.
DR PIR; B64667; B64667.
DR RefSeq; NP_207969.1; NC_000915.1.
DR RefSeq; WP_000187711.1; NC_018939.1.
DR PDB; 5LU0; X-ray; 1.73 A; A/B/C/D/E/F=1-233.
DR PDB; 5MX6; X-ray; 2.41 A; A/B/C/D/E/F=1-233.
DR PDB; 5MX8; X-ray; 2.40 A; A=1-233.
DR PDB; 6F4W; X-ray; 2.29 A; A/B/C/D/E/F=1-233.
DR PDB; 6F4X; X-ray; 1.69 A; A/B/C/D/E/F=1-233.
DR PDB; 6F52; X-ray; 2.00 A; A/B/C/D/E/F=1-233.
DR PDB; 6F5A; X-ray; 2.20 A; A/B/C/D/E/F=1-233.
DR PDB; 6F5I; X-ray; 2.30 A; A/B/C/D/E/F=1-233.
DR PDB; 6G7X; X-ray; 1.76 A; A/B/C/D/E/F=1-233.
DR PDBsum; 5LU0; -.
DR PDBsum; 5MX6; -.
DR PDBsum; 5MX8; -.
DR PDBsum; 6F4W; -.
DR PDBsum; 6F4X; -.
DR PDBsum; 6F52; -.
DR PDBsum; 6F5A; -.
DR PDBsum; 6F5I; -.
DR PDBsum; 6G7X; -.
DR AlphaFoldDB; P56463; -.
DR SMR; P56463; -.
DR IntAct; P56463; 1.
DR STRING; 85962.C694_06090; -.
DR PaxDb; P56463; -.
DR EnsemblBacteria; AAD08222; AAD08222; HP_1178.
DR KEGG; hpy:HP_1178; -.
DR PATRIC; fig|85962.47.peg.1266; -.
DR eggNOG; COG0813; Bacteria.
DR OMA; PQCLLCG; -.
DR PhylomeDB; P56463; -.
DR BRENDA; 2.4.2.1; 2604.
DR Proteomes; UP000000429; 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; 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..233
FT /note="Purine nucleoside phosphorylase DeoD-type"
FT /id="PRO_0000063137"
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..20
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 22..32
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 55..61
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 66..78
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 84..93
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 103..112
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 115..119
FT /evidence="ECO:0007829|PDB:6F4X"
FT TURN 120..122
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 131..144
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 149..155
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 167..172
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 175..181
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 182..191
FT /evidence="ECO:0007829|PDB:6F4X"
FT STRAND 195..205
FT /evidence="ECO:0007829|PDB:6F4X"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 214..219
FT /evidence="ECO:0007829|PDB:6F4X"
FT HELIX 222..232
FT /evidence="ECO:0007829|PDB:6F4X"
SQ SEQUENCE 233 AA; 25786 MW; 1E44E717F8BDAC9D CRC64;
MTPHINAKIG DFYPQCLLCG DPLRVSYIAK KFLQDAKEIT NVRNMLGFSG KYKGRGISLM
GHGMGIASCT IYVTELIKTY QVKELLRIGT CGAISPKVGL KDIIMATGAS TDSKTNRVRF
LNHDLSATPD FELSLRAYQT AKRLGIDLKV GNVFSSDFFY SFETHAFDLM AKYNHLAIEM
EAAGLYATAM ELNAKALCLC SVSDHLITKE ALSPKERVES FDNMIILALE MMS
