DEOD_ECO57
ID DEOD_ECO57 Reviewed; 239 AA.
AC P0ABP9; P09743;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 102.
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};
GN OrderedLocusNames=Z5986, ECs5343;
OS Escherichia coli O157:H7.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83334;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=O157:H7 / EDL933 / ATCC 700927 / EHEC;
RX PubMed=11206551; DOI=10.1038/35054089;
RA Perna N.T., Plunkett G. III, Burland V., Mau B., Glasner J.D., Rose D.J.,
RA Mayhew G.F., Evans P.S., Gregor J., Kirkpatrick H.A., Posfai G.,
RA Hackett J., Klink S., Boutin A., Shao Y., Miller L., Grotbeck E.J.,
RA Davis N.W., Lim A., Dimalanta E.T., Potamousis K., Apodaca J.,
RA Anantharaman T.S., Lin J., Yen G., Schwartz D.C., Welch R.A.,
RA Blattner F.R.;
RT "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.";
RL Nature 409:529-533(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=O157:H7 / Sakai / RIMD 0509952 / EHEC;
RX PubMed=11258796; DOI=10.1093/dnares/8.1.11;
RA Hayashi T., Makino K., Ohnishi M., Kurokawa K., Ishii K., Yokoyama K.,
RA Han C.-G., Ohtsubo E., Nakayama K., Murata T., Tanaka M., Tobe T., Iida T.,
RA Takami H., Honda T., Sasakawa C., Ogasawara N., Yasunaga T., Kuhara S.,
RA Shiba T., Hattori M., Shinagawa H.;
RT "Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and
RT genomic comparison with a laboratory strain K-12.";
RL DNA Res. 8:11-22(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEXES WITH PURINE NUCLEOSIDES
RP AND PHOSPHATE.
RX PubMed=12937174; DOI=10.1074/jbc.m304622200;
RA Bennett E.M., Li C., Allan P.W., Parker W.B., Ealick S.E.;
RT "Structural basis for substrate specificity of Escherichia coli purine
RT nucleoside phosphorylase.";
RL J. Biol. Chem. 278:47110-47118(2003).
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; AE005174; AAG59565.1; -; Genomic_DNA.
DR EMBL; BA000007; BAB38766.1; -; Genomic_DNA.
DR PIR; A86138; A86138.
DR PIR; G91296; G91296.
DR RefSeq; NP_313370.1; NC_002695.1.
DR RefSeq; WP_000224877.1; NZ_SWKA01000005.1.
DR PDB; 1PK7; X-ray; 2.50 A; A/B/C=2-238.
DR PDB; 1PK9; X-ray; 1.90 A; A/B/C=2-238.
DR PDB; 1PKE; X-ray; 2.30 A; A/B/C=2-238.
DR PDB; 1PR0; X-ray; 2.20 A; A/B/C=1-239.
DR PDB; 1PR1; X-ray; 2.30 A; A/B/C=1-239.
DR PDB; 1PR2; X-ray; 2.30 A; A/B/C=1-239.
DR PDB; 1PR4; X-ray; 2.40 A; A/B/C=1-239.
DR PDB; 1PR5; X-ray; 2.50 A; A/B/C=1-239.
DR PDB; 1PR6; X-ray; 2.10 A; A/B/C=1-239.
DR PDB; 1PW7; X-ray; 2.00 A; A/B/C=1-239.
DR PDBsum; 1PK7; -.
DR PDBsum; 1PK9; -.
DR PDBsum; 1PKE; -.
DR PDBsum; 1PR0; -.
DR PDBsum; 1PR1; -.
DR PDBsum; 1PR2; -.
DR PDBsum; 1PR4; -.
DR PDBsum; 1PR5; -.
DR PDBsum; 1PR6; -.
DR PDBsum; 1PW7; -.
DR AlphaFoldDB; P0ABP9; -.
DR SMR; P0ABP9; -.
DR STRING; 155864.EDL933_5728; -.
DR EnsemblBacteria; AAG59565; AAG59565; Z5986.
DR EnsemblBacteria; BAB38766; BAB38766; ECs_5343.
DR GeneID; 66671728; -.
DR GeneID; 913500; -.
DR KEGG; ece:Z5986; -.
DR KEGG; ecs:ECs_5343; -.
DR PATRIC; fig|386585.9.peg.5590; -.
DR eggNOG; COG0813; Bacteria.
DR HOGENOM; CLU_068457_2_0_6; -.
DR OMA; PQCLLCG; -.
DR Proteomes; UP000000558; Chromosome.
DR Proteomes; UP000002519; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProt.
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; Acetylation; Glycosyltransferase; Reference proteome;
KW Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..239
FT /note="Purine nucleoside phosphorylase DeoD-type"
FT /id="PRO_0000063131"
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:0000269|PubMed:12937174"
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:0000269|PubMed:12937174"
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:0000269|PubMed:12937174"
FT BINDING 44
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:12937174"
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:0000269|PubMed:12937174"
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:0000269|PubMed:12937174"
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:0000269|PubMed:12937174"
FT SITE 218
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT MOD_RES 27
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT STRAND 15..19
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 24..33
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 35..41
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 67..80
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 85..93
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 104..113
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:1PK9"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 132..144
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 166..173
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 183..192
FT /evidence="ECO:0007829|PDB:1PK9"
FT STRAND 196..205
FT /evidence="ECO:0007829|PDB:1PK9"
FT HELIX 215..237
FT /evidence="ECO:0007829|PDB:1PK9"
SQ SEQUENCE 239 AA; 25950 MW; 71D3DFAA5A176970 CRC64;
MATPHINAEM GDFADVVLMP GDPLRAKYIA ETFLEDAREV NNVRGMLGFT GTYKGRKISV
MGHGMGIPSC SIYTKELITD FGVKKIIRVG SCGAVLPHVK LRDVVIGMGA CTDSKVNRIR
FKDHDFAAIA DFDMVRNAVD AAKALGIDAR VGNLFSADLF YSPDGEMFDV MEKYGILGVE
MEAAGIYGVA AEFGAKALTI CTVSDHIRTH EQTTAAERQT TFNDMIKIAL ESVLLGDKE
