P0ABP8 (DEOD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Purine nucleoside phosphorylase DeoD-type
Short name=PNP
EC=2.4.2.1

Alternative name(s):
Inosine phosphorylase

Gene names

Name:	deoD
Synonyms:	pup
Ordered Locus Names:	b4384, JW4347

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	239 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules. HAMAP-Rule MF_01627
Catalytic activity	Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. HAMAP-Rule MF_01627
Subunit structure	Homohexamer.
Sequence similarities	Belongs to the PNP/UDP phosphorylase family.

Ontologies

Keywords
Molecular function	Glycosyltransferase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	purine nucleoside catabolic process Inferred from mutant phenotype PubMed 1089630. Source: EcoCyc purine nucleoside interconversion Inferred from direct assay PubMed 235429. Source: EcoCyc response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	purine-nucleoside phosphorylase activity Inferred from direct assay PubMed 235429. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-907568,EBI-907568

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 239

238

Purine nucleoside phosphorylase DeoD-type HAMAP-Rule MF_01627

PRO_0000063130

Amino acid modifications

Modified residue

27

1

N6-acetyllysine Ref.7

Secondary structure

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239

Helix Strand Turn

Details...

Beta strand

15 – 19

5

Helix

23 – 33

11

Beta strand

35 – 41

7

Helix

43 – 45

3

Beta strand

48 – 53

6

Beta strand

56 – 61

6

Helix

67 – 80

14

Beta strand

85 – 94

10

Beta strand

96 – 99

4

Beta strand

104 – 113

10

Helix

116 – 120

5

Turn

121 – 123

3

Helix

132 – 144

13

Beta strand

150 – 156

7

Helix

167 – 173

7

Beta strand

178 – 182

5

Helix

183 – 193

11

Beta strand

196 – 206

11

Turn

207 – 209

3

Helix

215 – 237

23

Sequences

	Sequence		Length	Mass (Da)
	P0ABP8 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 71D3DFAA5A176970	FASTA	239	25,950
	10 20 30 40 50 60 MATPHINAEM GDFADVVLMP GDPLRAKYIA ETFLEDAREV NNVRGMLGFT GTYKGRKISV 70 80 90 100 110 120 MGHGMGIPSC SIYTKELITD FGVKKIIRVG SCGAVLPHVK LRDVVIGMGA CTDSKVNRIR 130 140 150 160 170 180 FKDHDFAAIA DFDMVRNAVD AAKALGIDAR VGNLFSADLF YSPDGEMFDV MEKYGILGVE 190 200 210 220 230 MEAAGIYGVA AEFGAKALTI CTVSDHIRTH EQTTAAERQT TFNDMIKIAL ESVLLGDKE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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, 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).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

A27854. A41143.

RefSeq

NP_418801.1. NC_000913.2.
YP_492514.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A69	X-ray	2.10	A/B/C	2-239	[»]
1ECP	X-ray	2.00	A/B/C/D/E/F	2-239	[»]
1K9S	X-ray	2.00	A/B/C/D/E/F	2-237	[»]
1OTX	X-ray	2.70	A/B/C	2-238	[»]
1OTY	X-ray	2.50	A/B/C	2-238	[»]
1OU4	X-ray	2.50	A/B/C	2-238	[»]
1OUM	X-ray	2.40	A/B/C	2-238	[»]
1OV6	X-ray	2.40	A/B/C	2-238	[»]
1OVG	X-ray	2.20	A/B/C	2-238	[»]
3ONV	X-ray	1.89	A/B/C	2-238	[»]
3OOE	X-ray	2.00	A/B/C/D/E/F	2-238	[»]
3OOH	X-ray	2.90	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R	2-238	[»]
3OPV	X-ray	2.40	A/B/C/D/E/F/G/H/I/J/K/L	2-238	[»]
3UT6	X-ray	1.90	A/B/C	2-238	[»]

ProteinModelPortal

P0ABP8.

SMR

P0ABP8. Positions 2-238.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36195N.

IntAct

P0ABP8. 2 interactions.

STRING

511145.b4384.

2D gel databases

SWISS-2DPAGE

P0ABP8.

Proteomic databases

PaxDb

P0ABP8.

PRIDE

P0ABP8.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77337; AAC77337; b4384.
BAE78373; BAE78373; BAE78373.

GeneID

12934012.
945654.

KEGG

ecj:Y75_p4268.
eco:b4384.

PATRIC

32124384. VBIEscCol129921_4532.

Organism-specific databases

EchoBASE

EB0218.

EcoGene

EG10222. deoD.

Phylogenomic databases

eggNOG

COG0813.

HOGENOM

HOG000274896.

KO

K03784.

OMA

SFETHAF.

ProtClustDB

PRK05819.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0ABP8.

Family and domain databases

HAMAP

MF_01627. Pur_nucleosid_phosp.

InterPro

IPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]

PANTHER

PTHR21234. PTHR21234. 1 hit.

Pfam

PF01048. PNP_UDP_1. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00107. deoD. 1 hit.

PROSITE

PS01232. PNP_UDP_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00194. Vidarabine.

EvolutionaryTrace

P0ABP8.

Entry information

Entry name

DEOD_ECOLI

Accession

Primary (citable) accession number: P0ABP8
Secondary accession number(s): P09743, Q2M5T3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program