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Purine nucleoside phosphorylase DeoD-type (PNP) (EC 2.4.2.1) (Inosine phosphorylase)

 DEOD_ECOLI              Reviewed;         239 AA.
P0ABP8; P09743; Q2M5T3;
08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
25-OCT-2017, entry version 107.
RecName: Full=Purine nucleoside phosphorylase DeoD-type;
Short=PNP;
EC=2.4.2.1 {ECO:0000305|PubMed:11786017};
AltName: Full=Inosine phosphorylase;
Name=deoD; Synonyms=pup; OrderedLocusNames=b4384, JW4347;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=1714590; DOI=10.1073/pnas.88.16.7185;
Hershfield M.S., Chaffee S., Koro-Johnson L., Mary A., Smith A.A.,
Short S.A.;
"Use of site-directed mutagenesis to enhance the epitope-shielding
effect of covalent modification of proteins with polyethylene
glycol.";
Proc. Natl. Acad. Sci. U.S.A. 88:7185-7189(1991).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7610040; DOI=10.1093/nar/23.12.2105;
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.,
Blattner F.R.;
"Analysis of the Escherichia coli genome VI: DNA sequence of the
region from 92.8 through 100 minutes.";
Nucleic Acids Res. 23:2105-2119(1995).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 2-21.
PubMed=8506346; DOI=10.1073/pnas.90.11.5011;
Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C.,
Watanabe C.;
"Identifying proteins from two-dimensional gels by molecular mass
searching of peptide fragments in protein sequence databases.";
Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 225-239.
STRAIN=K12;
PubMed=3299264; DOI=10.1093/nar/15.13.5125;
Larsen J.E.L., Albrechtsen B., Valentin-Hansen P.;
"Analysis of the terminator region after the deoCABD operon of
Escherichia coli K-12 using a new class of single copy number operon-
fusion vectors.";
Nucleic Acids Res. 15:5125-5140(1987).
[7]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, AND IDENTIFICATION BY
MASS SPECTROMETRY.
STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
Grishin N.V., Zhao Y.;
"Lysine acetylation is a highly abundant and evolutionarily conserved
modification in Escherichia coli.";
Mol. Cell. Proteomics 8:215-225(2009).
[8]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed=9351810; DOI=10.1016/S0969-2126(97)00287-6;
Mao C., Cook W.J., Zhou M., Koszalka G.W., Krenitsky T.A.,
Ealick S.E.;
"The crystal structure of Escherichia coli purine nucleoside
phosphorylase: a comparison with the human enzyme reveals a conserved
topology.";
Structure 5:1373-1383(1997).
[9]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND SUBUNIT.
PubMed=9653038; DOI=10.1006/jmbi.1998.1799;
Koellner G., Luic M., Shugar D., Saenger W., Bzowska A.;
"Crystal structure of the ternary complex of E. coli purine nucleoside
phosphorylase with formycin B, a structural analogue of the substrate
inosine, and phosphate (sulphate) at 2.1-A resolution.";
J. Mol. Biol. 280:153-166(1998).
[10] {ECO:0000244|PDB:1K9S}
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 2-238 IN COMPLEX WITH
N(7)-METHYLFORMYCIN AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, AND
SUBUNIT.
PubMed=11786017; DOI=10.1006/jmbi.2001.5211;
Koellner G., Bzowska A., Wielgus-Kutrowska B., Luic M., Steiner T.,
Saenger W., Stepinski J.;
"Open and closed conformation of the E. coli purine nucleoside
phosphorylase active center and implications for the catalytic
mechanism.";
J. Mol. Biol. 315:351-371(2002).
-!- FUNCTION: Cleavage of guanosine or inosine to respective bases and
sugar-1-phosphate molecules. {ECO:0000269|PubMed:11786017}.
-!- CATALYTIC ACTIVITY: Purine nucleoside + phosphate = purine +
alpha-D-ribose 1-phosphate. {ECO:0000305|PubMed:11786017}.
-!- CATALYTIC ACTIVITY: Purine deoxynucleoside + phosphate = purine +
2'-deoxy-alpha-D-ribose 1-phosphate.
{ECO:0000305|PubMed:11786017}.
-!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:11786017,
ECO:0000269|PubMed:9653038}.
-!- INTERACTION:
Self; NbExp=7; IntAct=EBI-907568, EBI-907568;
-!- SIMILARITY: Belongs to the PNP/UDP phosphorylase family.
{ECO:0000305}.
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EMBL; M60917; AAA24401.1; -; Genomic_DNA.
EMBL; U14003; AAA97280.1; -; Genomic_DNA.
EMBL; U00096; AAC77337.1; -; Genomic_DNA.
EMBL; AP009048; BAE78373.1; -; Genomic_DNA.
EMBL; X05629; CAA29114.1; -; Genomic_DNA.
PIR; A41143; A27854.
RefSeq; NP_418801.1; NC_000913.3.
RefSeq; WP_000224877.1; NZ_LN832404.1.
PDB; 1A69; X-ray; 2.10 A; A/B/C=2-239.
PDB; 1ECP; X-ray; 2.00 A; A/B/C/D/E/F=2-239.
PDB; 1K9S; X-ray; 2.00 A; A/B/C/D/E/F=2-238.
PDB; 1OTX; X-ray; 2.70 A; A/B/C=2-239.
PDB; 1OTY; X-ray; 2.50 A; A/B/C=2-239.
PDB; 1OU4; X-ray; 2.50 A; A/B/C=2-239.
PDB; 1OUM; X-ray; 2.40 A; A/B/C=2-239.
PDB; 1OV6; X-ray; 2.40 A; A/B/C=2-239.
PDB; 1OVG; X-ray; 2.20 A; A/B/C=2-239.
PDB; 3ONV; X-ray; 1.89 A; A/B/C=2-238.
PDB; 3OOE; X-ray; 2.00 A; A/B/C/D/E/F=2-238.
PDB; 3OOH; X-ray; 2.90 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R=2-238.
PDB; 3OPV; X-ray; 2.40 A; A/B/C/D/E/F/G/H/I/J/K/L=2-238.
PDB; 3UT6; X-ray; 1.90 A; A/B/C=2-238.
PDB; 4TS3; X-ray; 2.30 A; A/B/C/D/E/F=2-238.
PDB; 4TS9; X-ray; 1.77 A; A/B/C=2-238.
PDB; 4TTA; X-ray; 2.00 A; A/B/C/D/E/F=2-238.
PDB; 4TTI; X-ray; 1.89 A; A/B/C/D/E/F=2-238.
PDB; 4TTJ; X-ray; 1.87 A; A/B/D=2-238.
PDB; 5I3C; X-ray; 2.32 A; A/B/C=2-238.
PDB; 5IU6; X-ray; 2.51 A; A/B/C=2-238.
PDBsum; 1A69; -.
PDBsum; 1ECP; -.
PDBsum; 1K9S; -.
PDBsum; 1OTX; -.
PDBsum; 1OTY; -.
PDBsum; 1OU4; -.
PDBsum; 1OUM; -.
PDBsum; 1OV6; -.
PDBsum; 1OVG; -.
PDBsum; 3ONV; -.
PDBsum; 3OOE; -.
PDBsum; 3OOH; -.
PDBsum; 3OPV; -.
PDBsum; 3UT6; -.
PDBsum; 4TS3; -.
PDBsum; 4TS9; -.
PDBsum; 4TTA; -.
PDBsum; 4TTI; -.
PDBsum; 4TTJ; -.
PDBsum; 5I3C; -.
PDBsum; 5IU6; -.
ProteinModelPortal; P0ABP8; -.
SMR; P0ABP8; -.
BioGrid; 4263006; 3.
DIP; DIP-36195N; -.
IntAct; P0ABP8; 2.
MINT; MINT-8328110; -.
STRING; 316385.ECDH10B_4542; -.
DrugBank; DB02947; 2-Fluoro-2'-Deoxyadenosine.
DrugBank; DB04441; 2-Fluoroadenosine.
DrugBank; DB03986; 6-Methyl-Formycin A.
DrugBank; DB02113; 6-Methylpurine.
DrugBank; DB03735; 9-(2-Deoxy-Beta-D-Ribofuranosyl)-6-Methylpurine.
DrugBank; DB02934; 9-(6-Deoxy-Alpha-L-Talofuranosyl)-6-Methylpurine.
DrugBank; DB03952; 9-(6-Deoxy-Beta-D-Allofuranosyl)-6-Methylpurine.
DrugBank; DB03528; 9-Beta-D-Xylofuranosyl-Adenine.
DrugBank; DB04198; Formycin B.
DrugBank; DB04335; Inosine.
DrugBank; DB02896; Methylthioinosine.
DrugBank; DB02066; N7-Methyl-Formycin A.
DrugBank; DB03172; Tubercidin.
iPTMnet; P0ABP8; -.
SWISS-2DPAGE; P0ABP8; -.
PaxDb; P0ABP8; -.
PRIDE; P0ABP8; -.
EnsemblBacteria; AAC77337; AAC77337; b4384.
EnsemblBacteria; BAE78373; BAE78373; BAE78373.
GeneID; 945654; -.
KEGG; ecj:JW4347; -.
KEGG; eco:b4384; -.
PATRIC; fig|1411691.4.peg.2301; -.
EchoBASE; EB0218; -.
EcoGene; EG10222; deoD.
eggNOG; ENOG4105D3A; Bacteria.
eggNOG; COG0813; LUCA.
HOGENOM; HOG000274896; -.
InParanoid; P0ABP8; -.
KO; K03784; -.
PhylomeDB; P0ABP8; -.
BioCyc; EcoCyc:DEOD-MONOMER; -.
BioCyc; MetaCyc:DEOD-MONOMER; -.
BRENDA; 2.4.2.1; 2026.
EvolutionaryTrace; P0ABP8; -.
PRO; PR:P0ABP8; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:UniProtKB.
GO; GO:0016020; C:membrane; IDA:UniProtKB.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IDA:EcoCyc.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
GO; GO:0006152; P:purine nucleoside catabolic process; IMP:EcoCyc.
GO; GO:0019686; P:purine nucleoside interconversion; IDA:EcoCyc.
HAMAP; MF_01627; Pur_nucleosid_phosp; 1.
InterPro; IPR004402; DeoD-type.
InterPro; IPR018016; Nucleoside_phosphorylase_CS.
InterPro; IPR000845; Nucleoside_phosphorylase_d.
InterPro; IPR035994; Nucleoside_phosphorylase_sf.
PANTHER; PTHR43691:SF2; PTHR43691:SF2; 1.
Pfam; PF01048; PNP_UDP_1; 1.
SUPFAM; SSF53167; SSF53167; 1.
TIGRFAMs; TIGR00107; deoD; 1.
PROSITE; PS01232; PNP_UDP_1; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Complete proteome;
Direct protein sequencing; Glycosyltransferase; Reference proteome;
Transferase.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:8506346}.
CHAIN 2 239 Purine nucleoside phosphorylase DeoD-
type.
/FTId=PRO_0000063130.
REGION 88 91 Phosphate binding.
{ECO:0000269|PubMed:11786017}.
REGION 180 182 Purine nucleoside binding.
{ECO:0000250|UniProtKB:P50389}.
REGION 204 205 Purine nucleoside binding.
{ECO:0000250|UniProtKB:P50389}.
BINDING 5 5 Purine nucleoside; shared with dimeric
partner. {ECO:0000250|UniProtKB:P50389}.
BINDING 21 21 Phosphate; via amide nitrogen.
{ECO:0000269|PubMed:11786017}.
BINDING 25 25 Phosphate. {ECO:0000269|PubMed:11786017}.
BINDING 44 44 Phosphate; shared with dimeric partner.
{ECO:0000269|PubMed:11786017}.
MOD_RES 27 27 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
STRAND 15 19 {ECO:0000244|PDB:4TS9}.
HELIX 23 33 {ECO:0000244|PDB:4TS9}.
STRAND 35 41 {ECO:0000244|PDB:4TS9}.
HELIX 43 45 {ECO:0000244|PDB:4TS9}.
STRAND 48 53 {ECO:0000244|PDB:4TS9}.
STRAND 56 61 {ECO:0000244|PDB:4TS9}.
HELIX 67 80 {ECO:0000244|PDB:4TS9}.
STRAND 85 94 {ECO:0000244|PDB:4TS9}.
STRAND 96 99 {ECO:0000244|PDB:3OOH}.
STRAND 104 113 {ECO:0000244|PDB:4TS9}.
HELIX 116 120 {ECO:0000244|PDB:4TS9}.
TURN 121 123 {ECO:0000244|PDB:4TS9}.
HELIX 132 145 {ECO:0000244|PDB:4TS9}.
STRAND 149 156 {ECO:0000244|PDB:4TS9}.
HELIX 167 173 {ECO:0000244|PDB:4TS9}.
STRAND 178 182 {ECO:0000244|PDB:4TS9}.
HELIX 183 193 {ECO:0000244|PDB:4TS9}.
STRAND 196 206 {ECO:0000244|PDB:4TS9}.
TURN 207 209 {ECO:0000244|PDB:4TS9}.
HELIX 215 220 {ECO:0000244|PDB:4TS9}.
HELIX 223 237 {ECO:0000244|PDB:4TS9}.
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


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