PDBsum entry 1tjs

Methyltransferase

PDB id: 1tjs

Contents

Protein chain

265 a.a.

Ligands

PO4

Waters ×99

References listed in PDB file

Key reference

• Title: The additivity of substrate fragments in enzyme-Ligand binding.
• Authors: T.J.Stout, C.R.Sage, R.M.Stroud.
• Ref.: Structure, 1998, 6, 839-848. [DOI no: 10.1016/S0969-2126(98)00086-0]
• PubMed id: 9687366

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 0%.

Abstract

BACKGROUND: Enzymes have evolved to recognise their target substrates with exquisite selectivity and specificity. Whether fragments of the substrate--perhaps never available to the evolving enzyme--are bound in the same manner as the parent substrate addresses the fundamental basis of specificity. An understanding of the relative contributions of individual portions of ligand molecules to the enzyme-binding interaction may offer considerable insight into the principles of substrate recognition. RESULTS: We report 12 crystal structures of Escherichia coli thymidylate synthase in complexes with available fragments of the substrate (dUMP), both with and without the presence of a cofactor analogue. The structures display considerable fidelity of binding mode and interactions. These complexes reveal several interesting features: the cofactor analogue enhances the localisation of substrate and substrate fragments near the reactive thiol; the ribose moiety reduces local disorder through additional specific enzyme-ligand interactions; the pyrimidine has multiple roles, ranging from stereospecificity to mechanistic competence; and the glycosidic linkage has an important role in the formation of a covalent attachment between substrate and enzyme. CONCLUSIONS: The requirements of ligand-protein binding can be understood in terms of the binding of separate fragments of the ligand. Fragments which are subsystems of the natural substrate for the enzyme confer specific contributions to the binding affinity, orientation or electrostatics of the enzymatic mechanism. This ligand-binding analysis provides a complementary method to the more prevalent approaches utilising site-directed mutagenesis. In addition, these observations suggest a modular approach for rational drug design utilising chemical fragments.

Figure 2.
Figure 2. The substrate fragments. The natural substrate of TS, dUMP (1), can be subdivided into several fragments, of which various combinations are commercially available. These include 2'-deoxyuridine (dUrd; 2), 2'5'-dideoxyuridine (ddUrd; 3), uridine (Urd; 4), phosphoribose (PR; 5), and phosphate (PO[4]^2-; 6).

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 839-848) copyright 1998.