P12758 (UDP_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Uridine phosphorylase
Short name=UPase
Short name=UrdPase
EC=2.4.2.3

Gene names

Name:	udp
Ordered Locus Names:	b3831, JW3808

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	253 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	Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Catalytic activity	Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
Pathway	Pyrimidine metabolism; UMP biosynthesis via salvage pathway; uracil from uridine (phosphorylase route): step 1/1.
Subunit structure	Homohexamer. The homohexamer shows 4-fold, 6-fold or 8-fold symmetry.
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the PNP/UDP phosphorylase family.

Ontologies

Keywords
Cellular component	Cytoplasm
Molecular function	Glycosyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	UMP salvage Inferred from electronic annotation. Source: UniProtKB-UniPathway nucleotide catabolic process Inferred from electronic annotation. Source: InterPro 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	uridine phosphorylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5 Ref.6 Ref.7

Chain

2 – 253

252

Uridine phosphorylase

PRO_0000063183

Experimental info

Mutagenesis

5

1

D → A, E or N: No change in activity. Ref.8

Sequence conflict

11

1

L → Y AA sequence Ref.7

Sequence conflict

15

1

D → Y AA sequence Ref.7

Secondary structure

1

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253

Helix Strand Turn

Details...

Beta strand

6 – 9

4

Helix

13 – 16

4

Beta strand

21 – 23

3

Helix

28 – 30

3

Helix

31 – 35

5

Beta strand

38 – 47

10

Beta strand

50 – 57

8

Beta strand

60 – 65

6

Helix

71 – 83

13

Beta strand

88 – 97

10

Beta strand

107 – 116

10

Helix

119 – 122

4

Helix

134 – 146

13

Beta strand

151 – 160

10

Helix

164 – 166

3

Beta strand

171 – 173

3

Helix

178 – 180

3

Helix

183 – 189

7

Beta strand

194 – 198

5

Helix

199 – 207

9

Turn

208 – 210

3

Beta strand

212 – 222

11

Turn

223 – 225

3

Helix

231 – 251

21

Sequences

	Sequence		Length	Mass (Da)
	P12758 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 7446DE45BA04D88D	FASTA	253	27,159
	10 20 30 40 50 60 MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF TTWRAELDGK 70 80 90 100 110 120 PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP HINVGDVLVT TASVRLDGAS 130 140 150 160 170 180 LHFAPLEFPA VADFECTTAL VEAAKSIGAT THVGVTASSD TFYPGQERYD TYSGRVVRHF 190 200 210 220 230 240 KGSMEEWQAM GVMNYEMESA TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH 250 AVKIVVEAAR RLL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene." Walton L., Richards C.A., Elwell L.P. Nucleic Acids Res. 17:6741-6741(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R. Science 257:771-778(1992) [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 2-18.
[6]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-12. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"FIS is a regulator of metabolism in Escherichia coli." Gonzalez-Gil G., Bringmann P., Kahmann R. Mol. Microbiol. 22:21-29(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-16. Strain: K12.
[8]	"Protein engineering of uridine phosphorylase from Escherichia coli K-12. I. Cloning and expression of uridine phosphorylase genes from Klebsiella aerogenes and Salmonella typhimurium in E. coli." Veiko V.P., Chebotaev D.V., Ovcharova I.V., Gul'Ko L.B. Bioorg. Khim. 24:381-387(1998) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-5.
[9]	"Atomic structure at 2.5-A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice." Morgunova E.Y., Mikhailov A.M., Popov A.N., Blagova E.V., Smirnova E.A., Vainshtein B.K., Mao C., Armstrong S.H.R., Ealick S.E., Komissarov A.A., Linkova E.V., Burlakova A.A., Mironov A.S., Debabov V.G. FEBS Lett. 367:183-187(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[10]	"Structure of Escherichia coli uridine phosphorylase at 2.0 A." Burling F.T., Kniewel R., Buglino J.A., Chadha T., Beckwith A., Lima C.D. Acta Crystallogr. D 59:73-76(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X15689 Genomic DNA. Translation: CAA33724.1.
M87049 Genomic DNA. Translation: AAA67626.1.
U00096 Genomic DNA. Translation: AAC76834.1.
AP009048 Genomic DNA. Translation: BAE77470.1.

PIR

S05491.

RefSeq

NP_418275.1. NC_000913.2.
YP_491611.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K3F	X-ray	2.50	A/B/C/D/E/F	1-253	[»]
1LX7	X-ray	2.00	A/B	1-253	[»]
1RXC	X-ray	2.35	A/B/C/D/E/F/G/H/I/J/K/L	1-253	[»]
1RXS	X-ray	2.80	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o	1-253	[»]
1RXU	X-ray	3.10	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R	1-253	[»]
1RXY	X-ray	1.70	A/B	1-253	[»]
1T0U	X-ray	2.20	A/B	1-253	[»]
1TGV	X-ray	2.20	A/B	1-253	[»]
1TGY	X-ray	2.20	A/B	1-253	[»]
1U1C	X-ray	2.20	A/B/C/D/E/F	2-252	[»]
1U1D	X-ray	2.00	A/B/C/D/E/F	2-252	[»]
1U1E	X-ray	2.00	A/B/C/D/E/F	2-252	[»]
1U1F	X-ray	2.30	A/B/C/D/E/F	2-252	[»]
1U1G	X-ray	1.95	A/B/C/D/E/F	2-252	[»]
3KVV	X-ray	1.80	A/B/C/D/E/F	1-253	[»]

ProteinModelPortal

P12758.

SMR

P12758. Positions 4-253.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11075N.

IntAct

P12758. 3 interactions.

STRING

511145.b3831.

2D gel databases

SWISS-2DPAGE

P12758.

Proteomic databases

PaxDb

P12758.

PRIDE

P12758.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76834; AAC76834; b3831.
BAE77470; BAE77470; BAE77470.

GeneID

12934305.
948987.

KEGG

ecj:Y75_p3347.
eco:b3831.

PATRIC

32123163. VBIEscCol129921_3947.

Organism-specific databases

EchoBASE

EB1038.

EcoGene

EG11045. udp.

Phylogenomic databases

eggNOG

COG2820.

HOGENOM

HOG000274897.

KO

K00757.

OMA

ICVEELA.

ProtClustDB

PRK11178.

Enzyme and pathway databases

BioCyc

EcoCyc:URPHOS-MONOMER.
ECOL316407:JW3808-MONOMER.
MetaCyc:URPHOS-MONOMER.

UniPathway

UPA00574; UER00633.

Gene expression databases

Genevestigator

P12758.

Family and domain databases

InterPro

IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
IPR010058. Uridine_phosphorylase.
[Graphical view]

PANTHER

PTHR21234. PTHR21234. 1 hit.

Pfam

PF01048. PNP_UDP_1. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01718. Uridine-psphlse. 1 hit.

PROSITE

PS01232. PNP_UDP_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00544. Fluorouracil.

EvolutionaryTrace

P12758.

Entry information

Entry name

UDP_ECOLI

Accession

Primary (citable) accession number: P12758
Secondary accession number(s): Q2M8D6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 137 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program