EzCatDB: T00038
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DB codeT00038
CATH domainDomain 11.20.970.10 : Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3Catalytic domain
Domain 23.40.1030.10 : Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2Catalytic domain
Domain 33.90.1170.30 : Aldehyde Oxidoreductase; domain 3
E.C.2.4.2.4
CSA1azy

CATH domainRelated DB codes (homologues)
1.20.970.10 : Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3T00037
3.40.1030.10 : Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2T00037
3.90.1170.30 : Aldehyde Oxidoreductase; domain 3T00037

Enzyme Name
UniProtKBKEGG

P07650
Protein nameThymidine phosphorylasethymidine phosphorylase
pyrimidine phosphorylase
thymidine-orthophosphate deoxyribosyltransferase
animal growth regulators, blood platelet-derived endothelial cellgrowth factors
blood platelet-derived endothelial cell growth factor
deoxythymidine phosphorylase
gliostatins
pyrimidine deoxynucleoside phosphorylase
thymidine:phosphate deoxy-D-ribosyltransferase
SynonymsEC 2.4.2.4
TdRPase
RefSeqNP_418799.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492512.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF02885 (Glycos_trans_3N)
PF00591 (Glycos_transf_3)
PF07831 (PYNP_C)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism
MAP00983Drug metabolism - other enzymes

UniProtKB:Accession NumberP07650
Entry nameTYPH_ECOLI
ActivityThymidine + phosphate = thymine + 2-deoxy- alpha-D-ribose 1-phosphate.
SubunitHomodimer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00214C00009C00178C00672
CompoundThymidineOrthophosphateThymine2-Deoxy-D-ribose 1-phosphate
Typeamide group,nucleosidephosphate group/phosphate ionamide group,aromatic ring (with nitrogen atoms)carbohydrate,phosphate group/phosphate ion
ChEBI17748
26078
17821
11563
PubChem5789
1004
22486802
1135
5460448
            
1azyA01UnboundUnboundUnboundUnbound
1azyB01UnboundUnboundUnboundUnbound
1otpA01UnboundUnboundUnboundUnbound
2tptA01UnboundUnboundUnboundUnbound
1azyA02UnboundUnboundUnboundUnbound
1azyB02UnboundUnboundUnboundUnbound
1otpA02UnboundUnboundUnboundUnbound
2tptA02UnboundAnalogue:SO4UnboundUnbound
1azyA03UnboundUnboundUnboundUnbound
1azyB03UnboundUnboundUnboundUnbound
1otpA03UnboundUnboundUnboundUnbound
2tptA03UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [3] & [5]
pdbCatalytic residues
         
1azyA01ARG 171;LYS 190
1azyB01ARG 171;LYS 190
1otpA01ARG 171;LYS 190
2tptA01ARG 171;LYS 190
1azyA02HIS  85
1azyB02HIS  85
1otpA02HIS  85
2tptA02HIS  85
1azyA03 
1azyB03 
1otpA03 
2tptA03 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.5
[4]Fig.12
[5]p.244, p.247-251, Fig.63

references
[1]
PubMed ID3546318
JournalJ Biol Chem
Year1987
Volume262
Pages3788-9
AuthorsCook WJ, Koszalka GW, Hall WW, Burns CL, Ealick SE
TitleCrystallization and preliminary x-ray investigation of thymidine phosphorylase from Escherichia coli.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID90338026
PubMed ID2199449
JournalJ Biol Chem
Year1990
Volume265
Pages14016-22
AuthorsWalter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE
TitleThree-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution.
Related UniProtKBP07650
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID98365499
PubMed ID9698549
JournalJ Mol Biol
Year1998
Volume281
Pages285-99
AuthorsPugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE
TitleStructural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.
Related PDB1azy,1otp,2tpt
Related UniProtKBP07650
[4]
PubMed ID10766296
JournalAnticancer Drug Des
Year1999
Volume14
Pages411-20
AuthorsCole C, Marks DS, Jaffar M, Stratford IJ, Douglas KT, Freeman S
TitleA similarity model for the human angiogenic factor, thymidine phosphorylase/platelet derived-endothelial cell growth factor.
[5]
PubMed ID10584069
JournalProteins
Year1999
Volume37
Pages242-52
AuthorsRick SW, Abashkin YG, Hilderbrandt RL, Burt SK
TitleComputational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase.
[6]
PubMed ID11042277
JournalFEBS Lett
Year2000
Volume483
Pages181-5
AuthorsBalzarini J, Degreve B, Esteban-Gamboa A, Esnouf R, De Clercq E, Engelborghs Y, Camarasa MJ, Perez-Perez MJ
TitleKinetic analysis of novel multisubstrate analogue inhibitors of thymidine phosphorylase.
[7]
PubMed ID12093726
JournalEMBO J
Year2002
Volume21
Pages3245-54
AuthorsMayans O, Ivens A, Nissen LJ, Kirschner K, Wilmanns M
TitleStructural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry.
[8]
PubMed ID12123839
JournalFEBS Lett
Year2002
Volume523
Pages239-46
AuthorsKim C, Xuong NH, Edwards S, Madhusudan, Yee MC, Spraggon G, Mills SE
TitleThe crystal structure of anthranilate phosphoribosyltransferase from the enterobacterium Pectobacterium carotovorum.
[9]
PubMed ID12459010
JournalJ Med Chem
Year2002
Volume45
Pages5426-9
AuthorsGuenther S, Balzarini J, De Clercq E, Nair V
TitleA thymidine phosphorylase-stable analogue of BVDU with significant antiviral activity.
[10]
PubMed ID11871876
JournalJ Org Chem
Year2002
Volume67
Pages1480-9
AuthorsOuwerkerk N, Steenweg M, de Ruijter M, Brouwer J, van Boom JH, Lugtenburg J, Raap J
TitleOne-pot two-step enzymatic coupling of pyrimidine bases to 2-deoxy-D-ribose-5-phosphate. A new strategy in the synthesis of stable isotope labeled deoxynucleosides.


createdupdated
2004-03-232009-02-26
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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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