1U71

Understanding the Role of Leu22 Variants in Methotrexate Resistance: Comparison of Wild-type and Leu22Arg Variant Mouse and Human Dihydrofolate Reductase Ternary Crystal Complexes with Methotrexate and NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Understanding the role of Leu22 variants in methotrexate resistance: comparison of wild-type and Leu22Arg variant mouse and human dihydrofolate reductase ternary crystal complexes with methotrexate and NADPH.

Cody, V.Luft, J.R.Pangborn, W.

(2005) Acta Crystallogr D Biol Crystallogr 61: 147-155

  • DOI: 10.1107/S0907444904030422
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Structural data are reported to 2.5 A resolution for the first full analysis of the methotrexate-resistant Leu22Arg (L22R) variant of mouse dihydrofolate reductase (mDHFR) crystallized as a ternary complex with methotrexate (MTX) and the cofactor NAD ...

    Structural data are reported to 2.5 A resolution for the first full analysis of the methotrexate-resistant Leu22Arg (L22R) variant of mouse dihydrofolate reductase (mDHFR) crystallized as a ternary complex with methotrexate (MTX) and the cofactor NADPH. These results are compared with the MTX and NADPH ternary complexes of L22R human DHFR (hDHFR) and those of mouse and human wild-type DHFR enzymes. The conformation of mDHFR Arg22 is such that it makes hydrogen-bonding contacts with Asp21, Trp24 and a structural water molecule, observations which were not made in the L22R hDHFR ternary complex. These data show that there is little difference between the structures of the wild type and L22R variant for either mouse or human DHFR; however, there are significant differences between the species. Comparison of these structures reveals that the active site of mDHFR is larger than that in the hDHFR structure. In mDHFR, the position of MTX is shifted 0.6 A toward helix C (residues 59-65), which in turn is shifted 1.2 A away from the active site relative to that observed in the hDHFR ternary complexes. In the L22R variant mDHFR structure, MTX makes shorter contacts to the conserved residues Ile7, Val115 and Tyr121 than in the L22R variant human DHFR structure. These contacts are comparable in both wild-type enzymes. The unexpected results from this comparison of the mouse and human DHFR complexes bound with the same ligand and cofactor illustrate the importance of detailed study of several species of enzyme, even when there is a high sequence homology between them. These data suggest that the differences in binding interactions of the L22R variant are in agreement with the weaker binding affinity for MTX in the variant enzymes; the larger size of the binding site in mDHFR supports the observation that the binding affinity of MTX for L22R mDHFR is significantly weaker than that of the L22R hDHFR enzyme.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, NY 14203, USA. cody@hwi.buffalo.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductaseA186Homo sapiensMutation(s): 1 
Gene Names: DHFR
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
MXA
Query on MXA

Download CCD File 
A
6-(2,5-DIMETHOXY-BENZYL)-5-METHYL-PYRIDO[2,3-D]PYRIMIDINE-2,4-DIAMINE
C17 H19 N5 O2
VJXSSYDSOJBUAV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MXAKi:  0.019999999552965164   nM  BindingDB
MXAIC50:  1   nM  BindingDB
MXAIC50:  15   nM  BindingDB
MXAIC50:  0.6100000143051147   nM  BindingDB
MXAKi:  33   nM  BindingDB
MXAKi :  33   nM  PDBBind
MXAIC50:  4.300000190734863   nM  BindingDB
MXAKi:  38   nM  BindingDB
MXAIC50:  2   nM  BindingDB
MXAIC50:  1.5   nM  BindingDB
MXAIC50:  4.400000095367432   nM  BindingDB
MXAIC50:  3   nM  BindingDB
MXAIC50:  3.299999952316284   nM  BindingDB
MXAIC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.144α = 90
b = 85.144β = 90
c = 78.042γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PROTEINmodel building
PROLSQrefinement
PROTEINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance