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Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.

Catalytic activityi

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate.

GO - Molecular functioni

  1. identical protein binding Source: IntAct
  2. purine-nucleoside phosphorylase activity Source: EcoCyc

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: EcoliWiki
  2. purine nucleoside catabolic process Source: EcoCyc
  3. purine nucleoside interconversion Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciEcoCyc:DEOD-MONOMER.
ECOL316407:JW4347-MONOMER.
MetaCyc:DEOD-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-type (EC:2.4.2.1)
Short name:
PNP
Alternative name(s):
Inosine phosphorylase
Gene namesi
Name:deoD
Synonyms:pup
Ordered Locus Names:b4384, JW4347
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10222. deoD.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. membrane Source: UniProtKB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 239238Purine nucleoside phosphorylase DeoD-typePRO_0000063130Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei27 – 271N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0ABP8.
PRIDEiP0ABP8.

2D gel databases

SWISS-2DPAGEP0ABP8.

Expressioni

Gene expression databases

GenevestigatoriP0ABP8.

Interactioni

Subunit structurei

Homohexamer.

Binary interactionsi

WithEntry#Exp.IntActNotes
itself7EBI-907568,EBI-907568

Protein-protein interaction databases

DIPiDIP-36195N.
IntActiP0ABP8. 2 interactions.
MINTiMINT-8328110.
STRINGi511145.b4384.

Structurei

Secondary structure

1
239
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 195Combined sources
Helixi23 – 3311Combined sources
Beta strandi35 – 417Combined sources
Helixi43 – 453Combined sources
Beta strandi48 – 536Combined sources
Beta strandi56 – 616Combined sources
Helixi67 – 8014Combined sources
Beta strandi85 – 9410Combined sources
Beta strandi96 – 994Combined sources
Beta strandi104 – 11310Combined sources
Helixi116 – 1205Combined sources
Turni121 – 1233Combined sources
Helixi132 – 14413Combined sources
Beta strandi150 – 1567Combined sources
Helixi167 – 1737Combined sources
Beta strandi178 – 1825Combined sources
Helixi183 – 19311Combined sources
Beta strandi196 – 20611Combined sources
Turni207 – 2093Combined sources
Helixi215 – 23723Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A69X-ray2.10A/B/C2-239[»]
1ECPX-ray2.00A/B/C/D/E/F2-239[»]
1K9SX-ray2.00A/B/C/D/E/F2-238[»]
1OTXX-ray2.70A/B/C2-239[»]
1OTYX-ray2.50A/B/C2-239[»]
1OU4X-ray2.50A/B/C2-239[»]
1OUMX-ray2.40A/B/C2-239[»]
1OV6X-ray2.40A/B/C2-239[»]
1OVGX-ray2.20A/B/C2-239[»]
3ONVX-ray1.89A/B/C2-238[»]
3OOEX-ray2.00A/B/C/D/E/F2-238[»]
3OOHX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R2-238[»]
3OPVX-ray2.40A/B/C/D/E/F/G/H/I/J/K/L2-238[»]
3UT6X-ray1.90A/B/C2-238[»]
ProteinModelPortaliP0ABP8.
SMRiP0ABP8. Positions 2-238.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ABP8.

Family & Domainsi

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.Curated

Phylogenomic databases

eggNOGiCOG0813.
HOGENOMiHOG000274896.
InParanoidiP0ABP8.
KOiK03784.
OMAiIRNDWPQ.
OrthoDBiEOG6BKJC5.
PhylomeDBiP0ABP8.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0ABP8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MATPHINAEM GDFADVVLMP GDPLRAKYIA ETFLEDAREV NNVRGMLGFT
60 70 80 90 100
GTYKGRKISV MGHGMGIPSC SIYTKELITD FGVKKIIRVG SCGAVLPHVK
110 120 130 140 150
LRDVVIGMGA CTDSKVNRIR FKDHDFAAIA DFDMVRNAVD AAKALGIDAR
160 170 180 190 200
VGNLFSADLF YSPDGEMFDV MEKYGILGVE MEAAGIYGVA AEFGAKALTI
210 220 230
CTVSDHIRTH EQTTAAERQT TFNDMIKIAL ESVLLGDKE
Length:239
Mass (Da):25,950
Last modified:January 23, 2007 - v2
Checksum:i71D3DFAA5A176970
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60917 Genomic DNA. Translation: AAA24401.1.
U14003 Genomic DNA. Translation: AAA97280.1.
U00096 Genomic DNA. Translation: AAC77337.1.
AP009048 Genomic DNA. Translation: BAE78373.1.
X05629 Genomic DNA. Translation: CAA29114.1.
PIRiA41143. A27854.
RefSeqiNP_418801.1. NC_000913.3.
YP_492514.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77337; AAC77337; b4384.
BAE78373; BAE78373; BAE78373.
GeneIDi12934012.
945654.
KEGGiecj:Y75_p4268.
eco:b4384.
PATRICi32124384. VBIEscCol129921_4532.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60917 Genomic DNA. Translation: AAA24401.1.
U14003 Genomic DNA. Translation: AAA97280.1.
U00096 Genomic DNA. Translation: AAC77337.1.
AP009048 Genomic DNA. Translation: BAE78373.1.
X05629 Genomic DNA. Translation: CAA29114.1.
PIRiA41143. A27854.
RefSeqiNP_418801.1. NC_000913.3.
YP_492514.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A69X-ray2.10A/B/C2-239[»]
1ECPX-ray2.00A/B/C/D/E/F2-239[»]
1K9SX-ray2.00A/B/C/D/E/F2-238[»]
1OTXX-ray2.70A/B/C2-239[»]
1OTYX-ray2.50A/B/C2-239[»]
1OU4X-ray2.50A/B/C2-239[»]
1OUMX-ray2.40A/B/C2-239[»]
1OV6X-ray2.40A/B/C2-239[»]
1OVGX-ray2.20A/B/C2-239[»]
3ONVX-ray1.89A/B/C2-238[»]
3OOEX-ray2.00A/B/C/D/E/F2-238[»]
3OOHX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R2-238[»]
3OPVX-ray2.40A/B/C/D/E/F/G/H/I/J/K/L2-238[»]
3UT6X-ray1.90A/B/C2-238[»]
ProteinModelPortaliP0ABP8.
SMRiP0ABP8. Positions 2-238.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-36195N.
IntActiP0ABP8. 2 interactions.
MINTiMINT-8328110.
STRINGi511145.b4384.

2D gel databases

SWISS-2DPAGEP0ABP8.

Proteomic databases

PaxDbiP0ABP8.
PRIDEiP0ABP8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77337; AAC77337; b4384.
BAE78373; BAE78373; BAE78373.
GeneIDi12934012.
945654.
KEGGiecj:Y75_p4268.
eco:b4384.
PATRICi32124384. VBIEscCol129921_4532.

Organism-specific databases

EchoBASEiEB0218.
EcoGeneiEG10222. deoD.

Phylogenomic databases

eggNOGiCOG0813.
HOGENOMiHOG000274896.
InParanoidiP0ABP8.
KOiK03784.
OMAiIRNDWPQ.
OrthoDBiEOG6BKJC5.
PhylomeDBiP0ABP8.

Enzyme and pathway databases

BioCyciEcoCyc:DEOD-MONOMER.
ECOL316407:JW4347-MONOMER.
MetaCyc:DEOD-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0ABP8.
PROiP0ABP8.

Gene expression databases

GenevestigatoriP0ABP8.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Use of site-directed mutagenesis to enhance the epitope-shielding effect of covalent modification of proteins with polyethylene glycol."
    Hershfield M.S., Chaffee S., Koro-Johnson L., Mary A., Smith A.A., Short S.A.
    Proc. Natl. Acad. Sci. U.S.A. 88:7185-7189(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases."
    Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.
    Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-21.
  6. "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."
    Larsen J.E.L., Albrechtsen B., Valentin-Hansen P.
    Nucleic Acids Res. 15:5125-5140(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 225-239.
    Strain: K12.
  7. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
  8. "The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology."
    Mao C., Cook W.J., Zhou M., Koszalka G.W., Krenitsky T.A., Ealick S.E.
    Structure 5:1373-1383(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
  9. "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."
    Koellner G., Luic M., Shugar D., Saenger W., Bzowska A.
    J. Mol. Biol. 280:153-166(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

Entry informationi

Entry nameiDEOD_ECOLI
AccessioniPrimary (citable) accession number: P0ABP8
Secondary accession number(s): P09743, Q2M5T3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 89 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.