1C3E

NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLATE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID.

Summary for 1C3E

• Entry DOI: 10.2210/pdb1c3e/pdb
• Related: 1c2t
• Descriptor: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE, 2-{4-[2-(2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL)-1-CARBOXY-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID, GLYCINAMIDE RIBONUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: purine biosynthesis, anti-cancer agent, inhibitor complex, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 47435.15

Authors

Greasley, S.E.,Yamashita, M.M.,Cai, H.,Benkovic, S.J.,Boger, D.L.,Wilson, I.A. (deposition date: 1999-07-27, release date: 1999-12-29, Last modification date: 2024-02-07)

Primary citation

Greasley, S.E.,Yamashita, M.M.,Cai, H.,Benkovic, S.J.,Boger, D.L.,Wilson, I.A.
New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid.
Biochemistry, 38:16783-16793, 1999

PubMed Abstract: The crystal structure of Escherichia coli GAR Tfase at 2.1 A resolution in complex with 10-formyl-5,8,10-trideazafolic acid (10-formyl-TDAF, K(i) = 260 nM), an inhibitor designed to form an enzyme-assembled multisubstrate adduct with the substrate, beta-GAR, was studied to determine the exact nature of its inhibitory properties. Rather than forming the expected covalent adduct, the folate inhibitor binds as the hydrated aldehyde (gem-diol) in the enzyme active site, in a manner that mimics the tetrahedral intermediate of the formyl transfer reaction. In this hydrated form, the inhibitor not only provides unexpected insights into the catalytic mechanism but also explains the 10-fold difference in inhibitor potency between 10-formyl-TDAF and the corresponding alcohol, and a further 10-fold difference for inhibitors that lack the alcohol. The presence of the hydrated aldehyde was confirmed in solution by (13)C-(1)H NMR spectroscopy of the ternary GAR Tfase-beta-GAR-10-formyl-TDAF complex using the (13)C-labeled 10-formyl-TDAF. This insight into the behavior of the inhibitor, which is analogous to protease or transaminase inhibitors, provides a novel and previously unrecognized basis for the design of more potent inhibitors of the folate-dependent formyl transfer enzymes of the purine biosynthetic pathway and development of anti-neoplastic agents.

PubMed: 10606510
DOI: 10.1021/bi991888a

Experimental method

X-RAY DIFFRACTION (2.1 Å)