P07650 (TYPH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Thymidine phosphorylase
EC=2.4.2.4

Alternative name(s):
TdRPase

Gene names

Name:	deoA
Synonyms:	tpp, ttg
Ordered Locus Names:	b4382, JW4345

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	440 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. HAMAP MF_01628
Catalytic activity	Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate. HAMAP MF_01628
Pathway	Pyrimidine metabolism; dTMP biosynthesis via salvage pathway; dTMP from thymine: step 1/2. HAMAP MF_01628
Subunit structure	Homodimer.
Sequence similarities	Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family.

Ontologies

Keywords
Molecular function	Glycosyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	pyrimidine base metabolic process Inferred from electronic annotation. Source: InterPro pyrimidine nucleoside metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	membrane Inferred from direct assay. Source: UniProtKB
Molecular function	pyrimidine-nucleoside phosphorylase activity Inferred from electronic annotation. Source: InterPro thymidine phosphorylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ygjK	P42592	1	EBI-909674,EBI-1121018

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 440

440

Thymidine phosphorylase HAMAP MF_01628

PRO_0000059054

Secondary structure

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440

Helix Strand Turn

Details...

Helix

4 – 12

9

Helix

19 – 30

12

Helix

36 – 49

14

Helix

53 – 64

12

Turn

73 – 76

4

Beta strand

81 – 86

6

Helix

94 – 103

10

Turn

104 – 106

3

Beta strand

108 – 113

6

Turn

117 – 119

3

Helix

123 – 126

4

Helix

127 – 129

3

Helix

139 – 148

10

Beta strand

150 – 155

6

Helix

163 – 173

11

Helix

180 – 191

12

Helix

192 – 194

3

Beta strand

197 – 206

10

Beta strand

210 – 213

4

Helix

214 – 230

17

Beta strand

234 – 241

8

Beta strand

246 – 252

7

Helix

253 – 263

11

Helix

270 – 286

17

Helix

293 – 305

13

Helix

308 – 319

12

Turn

324 – 328

5

Helix

330 – 332

3

Beta strand

338 – 343

6

Beta strand

349 – 354

6

Helix

356 – 365

10

Turn

366 – 368

3

Beta strand

371 – 374

4

Beta strand

382 – 385

4

Beta strand

392 – 394

3

Beta strand

399 – 406

8

Helix

407 – 420

14

Beta strand

421 – 426

6

Beta strand

433 – 438

6

Sequences

	Sequence		Length	Mass (Da)
	P07650 [UniParc]. Last modified February 1, 1995. Version 3. Checksum: 1DB3083C9275D2ED	FASTA	440	47,207
	10 20 30 40 50 60 MFLAQEIIRK KRDGHALSDE EIRFFINGIR DNTISEGQIA ALAMTIFFHD MTMPERVSLT 70 80 90 100 110 120 MAMRDSGTVL DWKSLHLNGP IVDKHSTGGV GDVTSLMLGP MVAACGGYIP MISGRGLGHT 130 140 150 160 170 180 GGTLDKLESI PGFDIFPDDN RFREIIKDVG VAIIGQTSSL APADKRFYAT RDITATVDSI 190 200 210 220 230 240 PLITASILAK KLAEGLDALV MDVKVGSGAF MPTYELSEAL AEAIVGVANG AGVRTTALLT 250 260 270 280 290 300 DMNQVLASSA GNAVEVREAV QFLTGEYRNP RLFDVTMALC VEMLISGKLA KDDAEARAKL 310 320 330 340 350 360 QAVLDNGKAA EVFGRMVAAQ KGPTDFVENY AKYLPTAMLT KAVYADTEGF VSEMDTRALG 370 380 390 400 410 420 MAVVAMGGGR RQASDTIDYS VGFTDMARLG DQVDGQRPLA VIHAKDENNW QEAAKAVKAA 430 440 IKLADKAPES TPTVYRRISE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: 7610040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The internal regulated promoter of the deo operon of Escherichia coli K-12." Valentin-Hansen P., Hammer K., Larsen J.E.L., Svendsen I. Nucleic Acids Res. 12:5211-5224(1984) [PubMed: 6087276] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 377-440. Strain: K12.
[5]	"Structure and function of the intercistronic regulatory deoC-deoA element of Escherichia coli K-12." Valentin-Hansen P., Hammer-Jespersen K., Boetius F., Svendsen I. EMBO J. 3:179-183(1984) [PubMed: 6323164] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-18.
[6]	"Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8-A resolution." Walter M.R., Cook W.J., Cole L.B., Short S.A., Koszalka G.W., Krenitsky T.A., Ealick S.E. J. Biol. Chem. 265:14016-14022(1990) [PubMed: 2199449] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[7]	"Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase." Pugmire M.J., Cook W.J., Jasanoff A., Walter M.R., Ealick S.E. J. Mol. Biol. 281:285-299(1998) [PubMed: 9698549] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U14003 Genomic DNA. Translation: AAA97278.1.
U00096 Genomic DNA. Translation: AAC77335.1.
AP009048 Genomic DNA. Translation: BAE78371.1.
X00742 Genomic DNA. Translation: CAA25324.1.
X03224 Genomic DNA. Translation: CAA26975.1.

PIR

S56606.

RefSeq

NP_418799.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AZY	X-ray	3.00	A/B	2-440	[»]
1OTP	X-ray	2.80	A	2-440	[»]
1TPT	X-ray	2.80	A	2-440	[»]
2TPT	X-ray	2.60	A	2-440	[»]

ProteinModelPortal

P07650.

SMR

P07650. Positions 1-440.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9426N.

IntAct

P07650. 4 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000226; EBESCP00000000226; EBESCG00000000185.
EBESCT00000017997; EBESCP00000017288; EBESCG00000017053.

GeneID

948901.

GenomeReviews

Gene locus JW4345 in contig AP009048_GR.
Gene locus b4382 in contig U00096_GR.

KEGG

ecj:JW4345.
eco:b4382.

PATRIC

32124380. VBIEscCol129921_4530.

Organism-specific databases

EchoBASE

EB0215.

EcoGene

EG10219. deoA.

Phylogenomic databases

eggNOG

COG0213.

GeneTree

EBGT00050000008921.

HOGENOM

HBG288505.

OMA

DMSTPLG.

PhylomeDB

P07650.

ProtClustDB

PRK05820.

Enzyme and pathway databases

BioCyc

EcoCyc:DEOA-MONOMER.
MetaCyc:DEOA-MONOMER.

Gene expression databases

Genevestigator

P07650.

Family and domain databases

HAMAP

MF_01628. Thymid_phosp.
[Tree]

InterPro

IPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N.
IPR020072. Glycosyl_Trfase_fam3_subgr_N.
IPR013102. PYNP_C.
IPR018090. Pyrmidine_PPas_bac/euk.
IPR000053. Pyrmidine_PPase.
IPR017872. Pyrmidine_PPase_CS.
IPR013465. Thymidine_Pase.
[Graphical view]

Gene3D

G3DSA:3.90.1170.30. G3DSA:3.90.1170.30. 1 hit.
G3DSA:1.20.970.10. Glyco_trans_3. 1 hit.
G3DSA:3.40.1030.10. Glyco_trans_3. 1 hit.

KO

K00758.

PANTHER

PTHR10515. Pyrmidine_PPase. 1 hit.

Pfam

PF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]

PIRSF

PIRSF000478. TP_PyNP. 1 hit.

SMART

SM00941. PYNP_C. 1 hit.
[Graphical view]

SUPFAM

SSF47648. Glyco_trans_3. 1 hit.
SSF52418. Glyco_trans_3. 1 hit.
SSF54680. PYNP_C. 1 hit.

TIGRFAMs

TIGR02643. T_phosphoryl. 1 hit.
TIGR02644. Y_phosphoryl. 1 hit.

PROSITE

PS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

TYPH_ECOLI

Accession

Primary (citable) accession number: P07650
Secondary accession number(s): Q2M5T5

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	February 1, 1995
Last modified:	January 25, 2012
This is version 119 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program