1DLS

METHOTREXATE-RESISTANT VARIANTS OF HUMAN DIHYDROFOLATE REDUCTASE WITH SUBSTITUTION OF LEUCINE 22: KINETICS, CRYSTALLOGRAPHY AND POTENTIAL AS SELECTABLE MARKERS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Methotrexate-resistant variants of human dihydrofolate reductase with substitutions of leucine 22. Kinetics, crystallography, and potential as selectable markers.

Lewis, W.S.Cody, V.Galitsky, N.Luft, J.R.Pangborn, W.Chunduru, S.K.Spencer, H.T.Appleman, J.R.Blakley, R.L.

(1995) J Biol Chem 270: 5057-5064

  • DOI: 10.1074/jbc.270.10.5057
  • Primary Citation of Related Structures:  
    1DLS, 1DLR

  • PubMed Abstract: 
  • Although substitution of tyrosine, phenylalanine, tryptophan, or arginine for leucine 22 in human dihydrofolate reductase greatly slows hydride transfer, there is little loss in overall activity (kcat) at pH 7.65 (except for the arginine 22 variant), but Km for dihydrofolate and NADPH are increased significantly ...

    Although substitution of tyrosine, phenylalanine, tryptophan, or arginine for leucine 22 in human dihydrofolate reductase greatly slows hydride transfer, there is little loss in overall activity (kcat) at pH 7.65 (except for the arginine 22 variant), but Km for dihydrofolate and NADPH are increased significantly. The greatest effect, decreased binding of methotrexate to the enzyme-NADPH complex by 740- to 28,000-fold due to a large increase in the rate of methotrexate dissociation, makes these variants suitable to act as selectable markers. Affinities for four other inhibitors are also greatly decreased. Binding of methotrexate to apoenzyme is decreased much less (decreases as much as 120-fold), binding of tetrahydrofolate is decreased as much as 23-fold, and binding of dihydrofolate is decreased little or increased. Crystal structures of ternary complexes of three of the variants show that the mutations cause little perturbation of the protein backbone, of side chains of other active site residues, or of bound inhibitor. The largest structural deviations occur in the ternary complex of the arginine variant at residues 21-27 and in the orientation of the methotrexate. Tyrosine 22 and arginine 22 relieve short contacts to methotrexate and NADPH by occupying low probability conformations, but this is unnecessary for phenylalanine 22 in the piritrexim complex.


    Related Citations: 
    • Methotrexate-Resistant Variants of Human Dihydrofolate Reductase: Effects of Phe-31 Substitutions
      Chunduru, S.K., Cody, V., Luft, J.R., Pangborn, W., Appleman, J.R., Blakley, R.L.
      (1994) J Biol Chem 269: 9547
    • Crystal Structure Determination at 2.3 Angstroms of Recombinant Human Dihydrofolate Reductase Ternary Complex with Nadph and Methotrexate-Gamma-Tetrazole
      Cody, V., Luft, J.R., Ciszak, E., Kalman, T.I., Freisheim, J.H.
      (1992) Anticancer Drug Des 7: 483

    Organizational Affiliation

    Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38101.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASEA186Homo sapiensMutation(s): 0 
Gene Names: POTENTIALDHFR
EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
PHAROS:  P00374
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
MTX (Subject of Investigation/LOI)
Query on MTX

Download Ideal Coordinates CCD File 
C [auth A]METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MTX Binding MOAD:  1DLS Ki: 10.9 (nM) from 1 assay(s)
BindingDB:  1DLS Ki: 0 (nM) from 1 assay(s)
Kd: 0.19 (nM) from 1 assay(s)
IC50: min: 0.6, max: 1500 (nM) from 61 assay(s)
EC50: min: 12.5, max: 13.3 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.156 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.496α = 90
b = 87.496β = 90
c = 76.733γ = 120
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance