1JKX

Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase.

Greasley, S.E.Marsilje, T.H.Cai, H.Baker, S.Benkovic, S.J.Boger, D.L.Wilson, I.A.

(2001) Biochemistry 40: 13538-13547

  • DOI: https://doi.org/10.1021/bi011482+
  • Primary Citation of Related Structures:  
    1JKX

  • PubMed Abstract: 

    Multisubstrate adduct inhibitors (MAI) of glycinamide ribonucleotide transformylase (GAR Tfase), which incorporate key features of the folate cofactor and the beta-GAR substrate, typically exhibit K(i)'s in the picomolar range. However, these compounds have reduced bioavailability due to the incorporation of a negatively charged phosphate moiety that prevents effective cellular uptake. Thus, a folate analogue that is capable of adduct formation with the substrate on the enzyme active site could lead to a potent GAR Tfase inhibitor that takes advantage of the cellular folate transport systems. We synthesized a dibromide folate analogue, 10-bromo-10-bromomethyl-5,8,10-trideazafolic acid, that was an intermediate designed to assemble with the substrate beta-GAR on the enzyme active site. We have now determined the crystal structure of the Escherichia coli GAR Tfase/MAI complex at 1.6 A resolution to ascertain the nature and mechanism of its time-dependent inhibition. The high-resolution crystal structure clearly revealed the existence of a covalent adduct between the substrate beta-GAR and the folate analogue (K(i) = 20 microM). However, the electron density map surprisingly indicated a C10 hydroxyl in the adduct rather than a bromide and suggested that the multisubstrate adduct is not formed directly from the dibromide but proceeds via an epoxide. Subsequently, we demonstrated the in situ conversion of the dibromide to the epoxide. Moreover, synthesis of the authentic epoxide confirmed that its inhibitory, time-dependent, and cytotoxic properties are comparable to those of the dibromide. Further, inhibition was strongest when the dibromide or epoxide is preincubated with both enzyme and substrate, indicating that inhibition occurs via the enzyme-dependent formation of the multisubstrate adduct. Thus, the crystal structure revealed the successful formation of an enzyme-assembled multisubstrate adduct and highlighted a potential application for epoxides, and perhaps aziridines, in the design of efficacious GAR Tfase inhibitors.


  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
A, B, C, D
212Escherichia coliMutation(s): 0 
Gene Names: PURN
EC: 2.1.2.2
UniProt
Find proteins for P08179 (Escherichia coli (strain K12))
Explore P08179 
Go to UniProtKB:  P08179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08179
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
138
Query on 138

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE
C30 H37 N6 O15 P
QZUCAWXKEZPFBV-PRICPSHJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.14α = 80.83
b = 56.01β = 71.71
c = 76.13γ = 83.69
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-05-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-03-13
    Changes: Source and taxonomy, Structure summary