PDBsum entry 2tpt

Transferase

PDB id: 2tpt

Contents

Protein chain

440 a.a. *

Ligands

SO4

* Residue conservation analysis

PDB id:

2tpt

Name:

Transferase

Title:

Structural and theoretical studies suggest domain movement produces an 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)

Resolution:

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

Date:

24-Nov-97 Release date: 02-Mar-99

Protein chain

P07650  (TYPH_ECOLI) -  Thymidine phosphorylase from Escherichia coli (strain K12)

Seq: 440 a.a.

Struc: 440 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.4.2.4 - thymidine phosphorylase.
• Reaction: thymidine + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + thymine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.

ABSTRACT

Two new crystal forms of Escherichia coli thymidine phosphorylase (EC 2.4.2.4) 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.