1GAR

TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT 1.96 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution.

Klein, C.Chen, P.Arevalo, J.H.Stura, E.A.Marolewski, A.Warren, M.S.Benkovic, S.J.Wilson, I.A.

(1995) J.Mol.Biol. 249: 153-175

  • DOI: 10.1006/jmbi.1995.0286

  • PubMed Abstract: 
  • An inhibitor complex structure of glycinamide ribonucleotide transformylase (GAR-Tfase; EC 2.1.2.2) from Escherichia coli has been determined with a multisubstrate adduct BW1476U89 to an R-value of 19.1% at 1.96 A resolution. The structure was determ ...

    An inhibitor complex structure of glycinamide ribonucleotide transformylase (GAR-Tfase; EC 2.1.2.2) from Escherichia coli has been determined with a multisubstrate adduct BW1476U89 to an R-value of 19.1% at 1.96 A resolution. The structure was determined by a combination of molecular and single isomorphous replacement using data from two different monoclinic crystal lattices and collecting data from crystals soaked in 20% (w/v) methyl-pentanediol as cryoprotectant for shock-freezing at -150 degrees C. The multisubstrate adduct is bound in an extended crevice at the interface between the two functional domains of the enzyme. This inhibitor is positioned in the binding site by three sets of tight interactions with its phosphate, glutamate and pyrimidone ring moieties, while its interventing linker atoms are more flexible and adopt two distinct sets of conformations. The highly conserved Arg103, His108 and Gln170 residues that are key in ligand binding and catalysis (His108), have compensatory conformational variation that gives some clues as to their role in substrate specificity and in the formyl transfer. The molecular design of 1476U89 as a multisubstrate adduct inhibitor (Ki approximately 100 pM at pH 8.5), is confirmed as it closely mimics the shape, molecular interaction and combined binding constants of the natural 10-formyltetrahydrofolate (10-CHO-H4F; Km approximately 77.4 microM at pH 8.5) and glycinamide-ribonucleotide (GAR; Km approximately 8.1 microM at pH 8.5) substrates. The stereochemistry of this ligand complex suggests that His108 may act as an electrophile stabilizing the oxyanion of the tetrahedral intermediate that is formed as a result of the direct attack on the 10-CHO-H4F by the amino group of GAR. Structural comparison of the folate binding modes among GAR-Tfase, dihydrofolate reductase and thymidylate synthase reveals that folate derivates bound to GAR-Tfase differentially adopt the trans conformation for the dihedral angle between atoms C-6 and C-9 providing a handle for targeting specific folate-dependent enzymes. The structural information derived from two different discrete conformations of the ligand in the binding site also suggests several leads for the de novo design of inhibitors of GAR-Tfase that may develop into useful chemotherapeutic agents.


    Related Citations: 
    • Crystal Structure of Glycinamide Ribonucleotide Transformylase from Escherichia Coli at 3.0 Angstroms Resolution. A Target Enzyme for Chemotherapy
      Chen, P.,Schulze-Gahmen, U.,Stura, E.A.,Inglese, J.,Johnson, D.L.,Marolewski, A.,Benkovic, S.J.,Wilson, I.A.
      (1992) J.Mol.Biol. 227: 283


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
A, B
212Escherichia coli (strain K12)Gene Names: purN
EC: 2.1.2.2
Find proteins for P08179 (Escherichia coli (strain K12))
Go to UniProtKB:  P08179
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U89
Query on U89

Download SDF File 
Download CCD File 
A, B
N-[4-[[3-(2,4-DIAMINO-1,6-DIHYDRO-6-OXO-4-PYRIMIDINYL)-PROPYL]-[2-((2-OXO-2-((4-PHOSPHORIBOXY)-BUTYL)-AMINO)-ETHYL)-THIO-ACETYL]-AMINO]BENZOYL]-1-GLUTAMIC ACID
C27 H38 N7 O12 P S
WIBNWPBCQGWSJV-IBGZPJMESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
U89Ki: 0.1 nM BINDINGMOAD
U89Ki: 0.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.700α = 90.00
b = 73.300β = 94.30
c = 35.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance