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PDBsum entry 1u72
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Oxidoreductase PDB id
1u72

 

 

 

 

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Contents
Protein chain
186 a.a. *
Ligands
NDP
MTX
Waters ×46
* Residue conservation analysis
PDB id:
1u72
Name: Oxidoreductase
Title: Understanding the role of leu22 variants in methotrexate resistance: comparison of wild-type and leu22arg variant mouse and human dihydrfolate reductase ternary crystal complexes with methotrexate and NADPH
Structure: Dihydrofolate reductase. Chain: a. Fragment: human dhfr. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dhfr. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.90Å     R-factor:   0.159     R-free:   0.213
Authors: V.Cody
Key ref:
V.Cody et al. (2005). 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. Acta Crystallogr D Biol Crystallogr, 61, 147-155. PubMed id: 15681865 DOI: 10.1107/S0907444904030422
Date:
02-Aug-04     Release date:   01-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00374  (DYR_HUMAN) -  Dihydrofolate reductase from Homo sapiens
Seq:
Struc: 		187 a.a.
186 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.1.3  - dihydrofolate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Folate Coenzymes
      Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+
(6S)-5,6,7,8-tetrahydrofolate
 +
NADP(+)
Bound ligand (Het Group name = NDP)
corresponds exactly 		=
7,8-dihydrofolate
Bound ligand (Het Group name = MTX)
matches with 91.18% similarity 		+ NADPH
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1107/S0907444904030422 Acta Crystallogr D Biol Crystallogr 61:147-155 (2005)
PubMed id: 15681865  
 
 
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.
V.Cody, J.R.Luft, W.Pangborn.
 
  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 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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superposition of the MTX-NADPH ternary DHFR complexes of L22R mDHFR (violet), L22R hDHFR (cyan), wild-type mDHFR (red) and wild-type hDHFR (green). Note the conformational changes in flexible loop regions. Residues Leu/Arg22, Glu30, Phe31, Gln35, Ser59 and Asn64 are shown. Drawings were made with SETOR (Evans, 1993[180] [Evans, S. V. (1993). J. Mol. Graph. 11, 134-138.]-[181][bluearr.gif] ). 		Figure 5.
Figure 5 (a) View of the Arg22 contacts for L22R mDHFR. Drawn with LIGPLOT (Wallace et al., 1995[236] [Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.]-[237][bluearr.gif] ). (b) View of the contacts to MTX for L22R mDHFR-MTX-NADPH complex. Note: Glu30 makes a hydrogen-bonding contact to MTX N1 and N2 that is not shown in this projection. Drawn with LIGPLOT (Wallace et al., 1995[238] [Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.]-[239][bluearr.gif] ).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 147-155) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360609 J.P.Volpato, N.Mayotte, E.Fossati, V.Guerrero, G.Sauvageau, and J.N.Pelletier (2011).
Selectively weakened binding of methotrexate by human dihydrofolate reductase allows rapid ex vivo selection of mammalian cells.
  J Mol Recognit, 24, 188-198.  
21302360 M.Sáez-Ayala, L.Sánchez-Del-Campo, M.F.Montenegro, S.Chazarra, A.Tárraga, J.Cabezas-Herrera, and J.N.Rodríguez-López (2011).
Comparison of a pair of synthetic tea-catechin-derived epimers: synthesis, antifolate activity, and tyrosinase-mediated activation in melanoma.
  ChemMedChem, 6, 440-449.  
20056546 A.Gangjee, H.D.Jain, J.Phan, X.Guo, S.F.Queener, and R.L.Kisliuk (2010).
2,4-Diamino-5-methyl-6-substituted arylthio-furo[2,3-d]pyrimidines as novel classical and nonclassical antifolates as potential dual thymidylate synthase and dihydrofolate reductase inhibitors.
  Bioorg Med Chem, 18, 953-961.  
18781689 A.R.Goerke, and J.R.Swartz (2009).
High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids.
  Biotechnol Bioeng, 102, 400-416.  
19374017 B.C.Bennett, Q.Wan, M.F.Ahmad, P.Langan, and C.G.Dealwis (2009).
X-ray structure of the ternary MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design.
  J Struct Biol, 166, 162-171.
PDB codes: 3dat 3dau
19478082 J.P.Volpato, B.J.Yachnin, J.Blanchet, V.Guerrero, L.Poulin, E.Fossati, A.M.Berghuis, and J.N.Pelletier (2009).
Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance.
  J Biol Chem, 284, 20079-20089.
PDB code: 3eig
18245389 A.Cavazzuti, G.Paglietti, W.N.Hunter, F.Gamarro, S.Piras, M.Loriga, S.Allecca, P.Corona, K.McLuskey, L.Tulloch, F.Gibellini, S.Ferrari, and M.P.Costi (2008).
Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development.
  Proc Natl Acad Sci U S A, 105, 1448-1453.
PDB codes: 2p8k 2qhx 3h4v
19003167 J.G.Affleck, and V.K.Walker (2008).
A role for Drosophila in understanding drug-induced cytotoxicity and teratogenesis.
  Cytotechnology, 57, 1-9.  
17078091 V.M.Popov, W.A.Yee, and A.C.Anderson (2007).
Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity.
  Proteins, 66, 375-387.  
17360617 Y.Kipnis, N.Papo, G.Haran, and A.Horovitz (2007).
Concerted ATP-induced allosteric transitions in GroEL facilitate release of protein substrate domains in an all-or-none manner.
  Proc Natl Acad Sci U S A, 104, 3119-3124.  
16451071 A.Gangjee, H.D.Jain, J.Phan, X.Lin, X.Song, J.J.McGuire, and R.L.Kisliuk (2006).
Dual inhibitors of thymidylate synthase and dihydrofolate reductase as antitumor agents: design, synthesis, and biological evaluation of classical and nonclassical pyrrolo[2,3-d]pyrimidine antifolates(1).
  J Med Chem, 49, 1055-1065.  
17019704 V.Cody, J.Pace, K.Chisum, and A.Rosowsky (2006).
New insights into DHFR interactions: analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5-(omega-carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions.
  Proteins, 65, 959-969.
PDB codes: 2fzh 2fzi 2fzj
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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