PDBsum entry 2tpt

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Transferase PDB id
Protein chain
440 a.a. *
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structural and theoretical studies suggest domain movement p active conformation of thymidine phosphorylase
Structure: Thymidine phosphorylase. Chain: a. Other_details: tetragonal crystal form
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12
Biol. unit: Dimer (from PDB file)
2.60Å     R-factor:   0.207     R-free:   0.244
Authors: M.J.Pugmire,W.J.Cook,A.Jasanoff,M.R.Walter,S.E.Ealick
Key ref:
M.J.Pugmire et al. (1998). Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase. J Mol Biol, 281, 285-299. PubMed id: 9698549 DOI: 10.1006/jmbi.1998.1941
24-Nov-97     Release date:   02-Mar-99    
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Protein chain
Pfam   ArchSchema ?
P07650  (TYPH_ECOLI) -  Thymidine phosphorylase
440 a.a.
440 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Thymidine phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate
+ phosphate
= thymine
+ 2-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     transferase activity     6 terms  


DOI no: 10.1006/jmbi.1998.1941 J Mol Biol 281:285-299 (1998)
PubMed id: 9698549  
Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.
M.J.Pugmire, W.J.Cook, A.Jasanoff, M.R.Walter, S.E.Ealick.
Two new crystal forms of Escherichia coli thymidine phosphorylase (EC have been found; a monoclinic form (space group P21) and an orthorhombic form (space group I222). These structures have been solved and compared to the previously determined tetragonal form (space group P43212). This comparison provides evidence of domain movement of the alpha (residues 1 to 65, 163 to 193) and alpha/beta (residues 80 to 154, 197 to 440) domains, which is thought to be critical for enzymatic activity by closing the active site cleft. Three hinge regions apparently allow the alpha and alpha/beta-domains to move relative to each other. The monoclinic model is the most open of the three models while the tetragonal model is the most closed. Phosphate binding induces formation of a hydrogen bond between His119 and Gly208, which helps to order the 115 to 120 loop that is disordered prior to phosphate binding. The formation of this hydrogen bond also appears to play a key role in the domain movement. The alpha-domain moves as a rigid body, while the alpha/beta-domain has some non-rigid body movement that is associated with the formation of the His119-Gly208 hydrogen bond. The 8 A distance between the two substrates reported for the tetragonal form indicates that it is probably not in an active conformation. However, the structural data for these two new crystal forms suggest that closing the interdomain cleft around the substrates may generate a functional active site. Molecular modeling and dynamics simulation techniques have been used to generate a hypothetical closed conformation of the enzyme. Analysis of this model suggests several residues of possible catalytic importance. The model explains observed kinetic results and satisfies requirements for efficient enzyme catalysis, most notably through the exclusion of water from the enzyme's active site.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Ribbon drawing of a monomer of the E. coli thymidine phosphorylase tetragonal crystal structure produced with the program INSIGHT II, v. 95.0 (Biosym Technologies Inc). a-Helices are labeled H1 to H17 and are represented as red cylinders. The two b-sheets are colored yellow and are labeled A and B. Phosphate and thymine are shown, indicating the location of the phosphate and thymidine binding sites. (b) Stereoview of a C^a trace of the TPT dimer, where the dimer axis is perpendicular to the plane of the page. Labels of every 20th residue position are included, where ` indicates the corresponding residue in the second subunit. This Figure was prodcued using MOLSCRIPT [Kraulis 1991].
Figure 2.
Figure 2. Stereoview of the phosphate binding site in the TPT model. Sulfate ion is likely bound in the phosphate binding site due to the high concentration of ammonium sulfate in the crystallization conditions. Possible hydrogen bonds are indicated by dotted lines. This Figure was prepared using the program MOLSCRIPT [Kraulis 1991].
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 281, 285-299) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19434693 A.Bronckaers, F.Gago, J.Balzarini, and S.Liekens (2009).
The dual role of thymidine phosphorylase in cancer development and chemotherapy.
  Med Res Rev, 29, 903-953.  
  17401202 K.Shimizu, and N.Kunishima (2007).
Purification, crystallization and preliminary X-ray diffraction study on pyrimidine nucleoside phosphorylase TTHA1771 from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 308-310.  
17309433 N.G.Panova, C.S.Alexeev, A.S.Kuzmichov, E.V.Shcheveleva, S.A.Gavryushov, K.M.Polyakov, A.M.Kritzyn, S.N.Mikhailov, R.S.Esipov, and A.I.Miroshnikov (2007).
Substrate specificity of Escherichia coli thymidine phosphorylase.
  Biochemistry (Mosc), 72, 21-28.  
15983408 W.Bu, E.C.Settembre, M.H.el Kouni, and S.E.Ealick (2005).
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
  Acta Crystallogr D Biol Crystallogr, 61, 863-872.
PDB codes: 1u1c 1u1d 1u1e 1u1f 1u1g
14725767 R.A.Norman, S.T.Barry, M.Bate, J.Breed, J.G.Colls, R.J.Ernill, R.W.Luke, C.A.Minshull, M.S.McAlister, E.J.McCall, H.H.McMiken, D.S.Paterson, D.Timms, J.A.Tucker, and R.A.Pauptit (2004).
Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor.
  Structure, 12, 75-84.
PDB code: 1uou
12093726 O.Mayans, A.Ivens, L.J.Nissen, K.Kirschner, and M.Wilmanns (2002).
Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry.
  EMBO J, 21, 3245-3254.
PDB codes: 1gxb 1o17
11489901 T.C.Appleby, I.I.Mathews, M.Porcelli, G.Cacciapuoti, and S.E.Ealick (2001).
Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
  J Biol Chem, 276, 39232-39242.
PDB codes: 1jds 1jdt 1jdu 1jdv 1jdz 1je0 1je1 1jp7 1jpv
10858450 J.Ishijima, T.Nakai, S.Kawaguchi, K.Hirotsu, and S.Kuramitsu (2000).
Free energy requirement for domain movement of an enzyme.
  J Biol Chem, 275, 18939-18945.
PDB codes: 1c9c 1cq6 1cq7 1cq8
9924029 I.Nishino, A.Spinazzola, and M.Hirano (1999).
Thymidine phosphorylase gene mutations in MNGIE, a human mitochondrial disorder.
  Science, 283, 689-692.  
10584069 S.W.Rick, Y.G.Abashkin, R.L.Hilderbrandt, and S.K.Burt (1999).
Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase.
  Proteins, 37, 242-252.  
9817849 M.J.Pugmire, and S.E.Ealick (1998).
The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.
  Structure, 6, 1467-1479.
PDB code: 1brw
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