1NCE

Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717

Summary for 1NCE

• Entry DOI: 10.2210/pdb1nce/pdb
• Related: 1bjg 1dna 1kce
• Descriptor: Thymidylate synthase, 2'-DEOXYURIDINE 5'-MONOPHOSPHATE, 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID, ... (4 entities in total)
• Functional Keywords: beta-sheet interface, protein-dump-cofactor analog complex, asymmetric dimer, biosynthetic protein
• Biological source: Escherichia coli, Escherichia coli O157:H7 (,)
• Cellular location: Cytoplasm : P0A884
• Total number of polymer chains: 2
• Total formula weight: 62666.74

Authors

Birdsall, D.L.,Finer-Moore, J.,Stroud, R.M. (deposition date: 2002-12-05, release date: 2002-12-25, Last modification date: 2024-11-20)

Primary citation

Birdsall, D.L.,Finer-Moore, J.,Stroud, R.M.
The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity.
Protein Eng., 16:229-240, 2003

PubMed Abstract: Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.

PubMed: 12702803
DOI: 10.1093/proeng/gzg020

Experimental method

X-RAY DIFFRACTION (2.4 Å)