PDBsum entry 1c3e

Transferase

PDB id: 1c3e

Contents

Protein chains

209 a.a. *

Ligands

NHR ×2

GAR ×2

Waters ×197

* Residue conservation analysis

PDB id:

1c3e

Name:

Transferase

Title:

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.

Structure:

Glycinamide ribonucleotide transformylase. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: purn. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.227 R-free: 0.263

Authors:

S.E.Greasley,M.M.Yamashita,H.Cai,S.J.Benkovic,D.L.Boger,I.A.Wilson

Key ref:

S.E.Greasley et al. (1999). 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. PubMed id: 10606510 DOI: 10.1021/bi991888a

Date:

27-Jul-99 Release date: 29-Dec-99

Protein chains

P08179  (PUR3_ECOLI) -  Phosphoribosylglycinamide formyltransferase from Escherichia coli (strain K12)

Seq: 212 a.a.

Struc: 209 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.2.2 - phosphoribosylglycinamide formyltransferase 1.
• Pathway: Purine Biosynthesis (early stages)
• Reaction: N₁-(5-phospho-beta-D-ribosyl)glycinamide + (6R)-10- formyltetrahydrofolate = N₂-formyl-N₁-(5-phospho-beta-D- ribosyl)glycinamide + (6S)-5,6,7,8-tetrahydrofolate + H⁺

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

Added reference

DOI no: 10.1021/bi991888a

Biochemistry 38:16783-16793 (1999)

PubMed id: 10606510

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.

S.E.Greasley, M.M.Yamashita, H.Cai, S.J.Benkovic, D.L.Boger, I.A.Wilson.

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.