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.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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.

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

(1999) Biochemistry 38: 16783-16793

  • Primary Citation of Related Structures:  

  • 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, b ...

    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.


    Related Citations: 
    • A pH Dependent Stabilization of an Active Site Loop Observed from Low and High pH Crystal Structures of Mutant Monomeric Glycinamide Ribonucleotide Transformylase at 1.8-1.9A
      Su, Y.,Yamashita, M.M.,Greasley, S.E.,Mullen, C.A.,Shim, J.H.,Jennings, P.A.,Benkovic, S.J.,Wilson, I.A.
      (1998) J.Mol.Biol. 281: 485
    • 10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF):a Potent Inhibitor of Glycinamide Ribonucleotide Transformylase.
      Boger, D.L.,Haynes, N.-E.,Kitos, P.A.,Ramcharan, J.,Marolewski, A.E.,Benkovic, S.J.
      (1997) Bioorg.Med.Chem. 5: 1817


    Organizational Affiliation

    Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
A, B
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: purN
EC: 2.1.2.2
Find proteins for P08179 (Escherichia coli (strain K12))
Go to UniProtKB:  P08179
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAR
Query on GAR

Download SDF File 
Download CCD File 
A, B
GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L
 Ligand Interaction
NHR
Query on NHR

Download SDF File 
Download CCD File 
A, B
2-{4-[2-(2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL)-1-CARBOXY-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID
(10R)-10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID
C23 H22 N4 O8
DAOQLLQRJAXMGY-PBHICJAKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NHRKi: 260 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.250α = 90.00
b = 112.790β = 101.50
c = 46.960γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation