Thymidine phosphorylase - Escherichia coli (strain K12)

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P07650 (TYPH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 132. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome] [HAMAP]

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-Rule MF_01628
Catalytic activity	Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate. HAMAP-Rule MF_01628
Pathway	Pyrimidine metabolism; dTMP biosynthesis via salvage pathway; dTMP from thymine: step 1/2. HAMAP-Rule 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 nucleobase metabolic process Inferred from electronic annotation. Source: InterPro response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki thymidine metabolic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	phosphorylase activity Inferred from electronic annotation. Source: InterPro pyrimidine-nucleoside phosphorylase activity Inferred from electronic annotation. Source: InterPro thymidine phosphorylase activity Inferred from electronic annotation. Source: HAMAP
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-Rule MF_01628

PRO_0000059054

Secondary structure

440

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P07650 [UniParc].

Last modified February 1, 1995. Version 3.
Checksum: 1DB3083C9275D2ED
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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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).

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.
YP_492512.1. NC_007779.1.

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. 2 interactions.

STRING

511145.b4382.

Proteomic databases

PaxDb

P07650.

PRIDE

P07650.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77335; AAC77335; b4382.
BAE78371; BAE78371; BAE78371.

GeneID

12933785.
948901.

KEGG

ecj:Y75_p4266.
eco:b4382.

PATRIC

32124380. VBIEscCol129921_4530.

Organism-specific databases

EchoBASE

EB0215.

EcoGene

EG10219. deoA.

Phylogenomic databases

eggNOG

COG0213.

HOGENOM

HOG000047313.

K00758.

OMA

LMAIYFR.

ProtClustDB

PRK05820.

Enzyme and pathway databases

BioCyc

EcoCyc:DEOA-MONOMER.
ECOL316407:JW4345-MONOMER.
MetaCyc:DEOA-MONOMER.

UniPathway

UPA00578; UER00638.

Gene expression databases

Genevestigator

P07650.

Family and domain databases

Gene3D

3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.

HAMAP

MF_01628. Thymid_phosp.

InterPro

IPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N_dom.
IPR013102. PYNP_C.
IPR018090. Pyrmidine_PPas_bac/euk.
IPR000053. Pyrmidine_PPase.
IPR017872. Pyrmidine_PPase_CS.
IPR013465. Thymidine_Pase.
[Graphical view]

PANTHER

PTHR10515. PTHR10515. 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...

Other

BindingDB

P07650.

ChEMBL

CHEMBL3726.

EvolutionaryTrace

P07650.

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:	May 1, 2013
This is version 132 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents