DB code: T00038

CATH domain 1.20.970.10 : Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 Catalytic domain
3.40.1030.10 : Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 Catalytic domain
3.90.1170.30 : Aldehyde Oxidoreductase; domain 3
E.C. 2.4.2.4
CSA 1azy
M-CSA 1azy
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P07650 Thymidine phosphorylase
EC 2.4.2.4
TdRPase
NP_418799.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492512.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF02885 (Glycos_trans_3N)
PF00591 (Glycos_transf_3)
PF07831 (PYNP_C)
[Graphical View]

KEGG enzyme name
thymidine 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07650 TYPH_ECOLI Thymidine + phosphate = thymine + 2-deoxy- alpha-D-ribose 1-phosphate. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00240 Pyrimidine metabolism
MAP00983 Drug metabolism - other enzymes

Compound table
Substrates Products Intermediates
KEGG-id C00214 C00009 C00178 C00672
E.C.
Compound Thymidine Orthophosphate Thymine 2-Deoxy-D-ribose 1-phosphate
Type amide group,nucleoside phosphate group/phosphate ion amide group,aromatic ring (with nitrogen atoms) carbohydrate,phosphate group/phosphate ion
ChEBI 17748
26078
17821
11563
PubChem 5789
1004
22486802
1135
5460448
1azyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1azyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1otpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2tptA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1azyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1azyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1otpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2tptA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound
1azyA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1azyB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1otpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2tptA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3] & [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1azyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 171;LYS 190
1azyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 171;LYS 190
1otpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 171;LYS 190
2tptA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 171;LYS 190
1azyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 85
1azyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 85
1otpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 85
2tptA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 85
1azyA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1azyB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1otpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2tptA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Fig.5
[4]
Fig.1 2
[5]
p.244, p.247-251, Fig.6 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 3546318
Journal J Biol Chem
Year 1987
Volume 262
Pages 3788-9
Authors Cook WJ, Koszalka GW, Hall WW, Burns CL, Ealick SE
Title Crystallization and preliminary x-ray investigation of thymidine phosphorylase from Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID 90338026
PubMed ID 2199449
Journal J Biol Chem
Year 1990
Volume 265
Pages 14016-22
Authors Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE
Title Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution.
Related PDB
Related UniProtKB P07650
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID 98365499
PubMed ID 9698549
Journal J Mol Biol
Year 1998
Volume 281
Pages 285-99
Authors Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE
Title Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.
Related PDB 1azy 1otp 2tpt
Related UniProtKB P07650
[4]
Resource
Comments
Medline ID
PubMed ID 10766296
Journal Anticancer Drug Des
Year 1999
Volume 14
Pages 411-20
Authors Cole C, Marks DS, Jaffar M, Stratford IJ, Douglas KT, Freeman S
Title A similarity model for the human angiogenic factor, thymidine phosphorylase/platelet derived-endothelial cell growth factor.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10584069
Journal Proteins
Year 1999
Volume 37
Pages 242-52
Authors Rick SW, Abashkin YG, Hilderbrandt RL, Burt SK
Title Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 11042277
Journal FEBS Lett
Year 2000
Volume 483
Pages 181-5
Authors Balzarini J, Degreve B, Esteban-Gamboa A, Esnouf R, De Clercq E, Engelborghs Y, Camarasa MJ, Perez-Perez MJ
Title Kinetic analysis of novel multisubstrate analogue inhibitors of thymidine phosphorylase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12093726
Journal EMBO J
Year 2002
Volume 21
Pages 3245-54
Authors Mayans O, Ivens A, Nissen LJ, Kirschner K, Wilmanns M
Title Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 12123839
Journal FEBS Lett
Year 2002
Volume 523
Pages 239-46
Authors Kim C, Xuong NH, Edwards S, Madhusudan, Yee MC, Spraggon G, Mills SE
Title The crystal structure of anthranilate phosphoribosyltransferase from the enterobacterium Pectobacterium carotovorum.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12459010
Journal J Med Chem
Year 2002
Volume 45
Pages 5426-9
Authors Guenther S, Balzarini J, De Clercq E, Nair V
Title A thymidine phosphorylase-stable analogue of BVDU with significant antiviral activity.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11871876
Journal J Org Chem
Year 2002
Volume 67
Pages 1480-9
Authors Ouwerkerk N, Steenweg M, de Ruijter M, Brouwer J, van Boom JH, Lugtenburg J, Raap J
Title One-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.
Related PDB
Related UniProtKB

Comments

Created Updated
2004-03-23 2009-02-26