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
  • Structures With Same Primary Citation

  • 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), ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASEA186Homo sapiensMutation(s): 0 
Gene Names: POTENTIALDHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
NIH Common Fund Data Resources
PHAROS  P00374
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
MTX
Query on MTX

Download CCD File 
A
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTXIC50:  4   nM  BindingDB
MTXEC50:  12.5   nM  BindingDB
MTXIC50:  13.800000190734863   nM  BindingDB
MTXIC50:  720   nM  BindingDB
MTXIC50:  0.699999988079071   nM  BindingDB
MTXIC50:  2   nM  BindingDB
MTXIC50:  1.5   nM  BindingDB
MTXIC50:  7.900000095367432   nM  BindingDB
MTXIC50:  1   nM  BindingDB
MTXIC50:  4.599999904632568   nM  BindingDB
MTXIC50:  4.599999904632568   nM  BindingDB
MTXIC50:  80   nM  BindingDB
MTXIC50:  9.600000381469727   nM  BindingDB
MTXIC50:  3.799999952316284   nM  BindingDB
MTXEC50:  13.300000190734863   nM  BindingDB
MTXIC50:  2.0999999046325684   nM  BindingDB
MTXIC50:  3.299999952316284   nM  BindingDB
MTXIC50:  3   nM  BindingDB
MTXIC50:  2.5   nM  BindingDB
MTXIC50:  6.599999904632568   nM  BindingDB
MTXIC50:  0.8199999928474426   nM  BindingDB
MTXIC50:  1.399999976158142   nM  BindingDB
MTXIC50:  6.699999809265137   nM  BindingDB
MTXIC50:  66   nM  BindingDB
MTXIC50:  80   nM  BindingDB
MTXIC50:  44   nM  BindingDB
MTXIC50:  1.7000000476837158   nM  BindingDB
MTXIC50:  73   nM  BindingDB
MTXIC50:  3.9000000953674316   nM  BindingDB
MTXIC50:  30   nM  BindingDB
MTXIC50:  35   nM  BindingDB
MTXIC50:  38   nM  BindingDB
MTXIC50:  40   nM  BindingDB
MTXIC50:  22   nM  BindingDB
MTXIC50:  24   nM  BindingDB
MTXIC50:  25   nM  BindingDB
MTXIC50:  26   nM  BindingDB
MTXIC50:  3.4000000953674316   nM  BindingDB
MTXIC50:  14.5   nM  BindingDB
MTXIC50:  2.700000047683716   nM  BindingDB
MTXIC50:  32.939998626708984   nM  BindingDB
MTXKi:  10.899999618530273   nM  Binding MOAD
MTXIC50:  0.6000000238418579   nM  BindingDB
MTXIC50:  18   nM  BindingDB
MTXIC50:  0.7200000286102295   nM  BindingDB
MTXIC50:  20   nM  BindingDB
MTXIC50:  24.299999237060547   nM  BindingDB
MTXKi:  0   nM  BindingDB
MTXIC50:  8   nM  BindingDB
MTXIC50:  11   nM  BindingDB
MTXIC50:  25   nM  BindingDB
MTXIC50:  20   nM  BindingDB
MTXIC50:  1.7000000476837158   nM  BindingDB
MTXIC50:  35   nM  BindingDB
MTXIC50:  1.2000000476837158   nM  BindingDB
MTXIC50:  1.600000023841858   nM  BindingDB
MTXIC50:  9   nM  BindingDB
MTXIC50:  50   nM  BindingDB
MTXIC50:  1500   nM  BindingDB
MTXIC50:  6   nM  BindingDB
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 

  • 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