3N0H

hDHFR double mutant Q35S/N64F Trimethoprim Binary Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic analysis reveals a novel second binding site for trimethoprim in active site double mutants of human dihydrofolate reductase.

Cody, V.Pace, J.Piraino, J.Queener, S.F.

(2011) J.Struct.Biol. 176: 52-59

  • DOI: 10.1016/j.jsb.2011.06.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to produce a more potent replacement for trimethoprim (TMP) used as a therapy for Pneumocystis pneumonia and targets dihydrofolate reductase from Pneumocystis jirovecii (pjDHFR), it is necessary to understand the determinants of potency and ...

    In order to produce a more potent replacement for trimethoprim (TMP) used as a therapy for Pneumocystis pneumonia and targets dihydrofolate reductase from Pneumocystis jirovecii (pjDHFR), it is necessary to understand the determinants of potency and selectivity against DHFR from the mammalian host and fungal pathogen cells. To this end, active site residues in human (h) DHFR were replaced with those from pjDHFR. Structural data are reported for two complexes of TMP with the double mutants Gln35Ser/Asn64Phe (Q35S/N64F) and Gln35Lys/Asn64Phe (Q35K/N64F) of hDHFR that unexpectedly show evidence for the binding of two molecules of TMP: one molecule that binds in the normal folate binding site and the second molecule that binds in a novel subpocket site such that the mutated residue Phe64 is involved in van der Waals contacts to the trimethoxyphenyl ring of the second TMP molecule. Kinetic data for the binding of TMP to hDHFR and pjDHFR reveal an 84-fold selectivity of TMP against pjDHFR (K(i) 49 nM) compared to hDHFR (K(i) 4093 nM). Two mutants that contain one substitution from pj--and one from the closely related Pneumocystis carinii DHFR (pcDHFR) (Q35K/N64F and Q35S/N64F) show K(i) values of 593 and 617 nM, respectively; these K(i) values are well above both the K(i) for pjDHFR and are similar to pcDHFR (Q35K/N64F and Q35S/N64F) (305nM). These results suggest that active site residues 35 and 64 play key roles in determining selectivity for pneumocystis DHFR, but that other residues contribute to the unique binding of inhibitors to these enzymes.


    Organizational Affiliation

    Structural Biology Department, Hauptman Woodward Medical Research Institute, 700 Ellicott St. Buffalo, NY 14203, USA. cody@hwi.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
186Homo sapiensMutation(s): 2 
Gene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Go to Gene View: DHFR
Go to UniProtKB:  P00374
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TOP
Query on TOP

Download SDF File 
Download CCD File 
A
TRIMETHOPRIM
C14 H18 N4 O3
IEDVJHCEMCRBQM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TOPKi: 6 - 45784 nM (98) BINDINGDB
TOPIC50: 27 - 270000 nM (98) BINDINGDB
TOPKi: 617 nM BINDINGMOAD
TOPKi: 617 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 84.016α = 90.00
b = 84.016β = 90.00
c = 78.495γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-14 
  • Released Date: 2011-09-28 
  • Deposition Author(s): Cody, V.

Revision History 

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description