5DFR

CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding.

Bystroff, C.Kraut, J.

(1991) Biochemistry 30: 2227-2239

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of unliganded dihydrofolate reductase (DHFR) from Escherichia coli has been solved and refined to an R factor of 19% at 2.3-A resolution in a crystal form that is nonisomorphous with each of the previously reported E. coli DHFR ...

    The crystal structure of unliganded dihydrofolate reductase (DHFR) from Escherichia coli has been solved and refined to an R factor of 19% at 2.3-A resolution in a crystal form that is nonisomorphous with each of the previously reported E. coli DHFR crystal structures [Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, B. C., & Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662; Bystroff, C., Oatley, S. J., & Kraut, J. (1990) Biochemistry 29, 3263-3277]. Significant conformational changes occur between the apoenzyme and each of the complexes: the NADP+ holoenzyme, the folate-NADP+ ternary complex, and the methotrexate (MTX) binary complex. The changes are small, with the largest about 3 A and most of them less than 1 A. For simplicity a two-domain description is adopted in which one domain contains the NADP+ 2'-phosphate binding site and the binding sites for the rest of the coenzyme and for the substrate lie between the two domains. Binding of either NADP+ or MTX induces a closing of the PABG-binding cleft and realignment of alpha-helices C and F which bind the pyrophosphate of the coenzyme. Formation of the ternary complex from the holoenzyme does not involve further relative domain shifts but does involve a shift of alpha-helix B and a floppy loop (the Met-20 loop) that precedes alpha B. These observations suggest a mechanism for cooperativity in binding between substrate and coenzyme wherein the greatest degree of cooperativity is expressed in the transition-state complex. We explore the idea that the MTX binary complex in some ways resembles the transition-state complex.


    Related Citations: 
    • Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
      Bolin, J.T.,Filman, D.J.,Matthews, D.A.,Hamlin, R.C.,Kraut, J.
      (1982) J.Biol.Chem. 257: 13650
    • Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with Methotrexate and on Chemical Modifications
      Poe, M.,Hoogsteen, K.,Matthews, D.A.
      (1979) J.Biol.Chem. 254: 8143
    • Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
      Matthews, D.A.,Alden, R.A.,Bolin, J.T.,Filman, D.J.,Freer, S.T.,Hamlin, R.,Hol, W.G.J.,Kisliuk, R.L.,Pastore, E.J.,Plante, L.T.,Xuong, N.-H.,Kraut, J.
      (1978) J.Biol.Chem. 253: 6946
    • Crystal Structures of Escherichia Coli Dihydrofolate Reductase. The Nadp+ Holoenzyme and the Folate(Dot)Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State
      Bystroff, C.,Oatley, S.J.,Kraut, J.
      (1990) Biochemistry 29: 3263
    • Effect of Single Amino Acid Replacements on the Folding and Stability of Dihydrofolate Reductase from Escherichia Coli
      Perry, K.M.,Onuffer, J.J.,Touchette, N.A.,Herndon, C.S.,Gittelman, M.S.,Matthews, C.R.,Chen, J.-T.,Mayer, R.J.,Taira, K.,Benkovic, S.J.,Howell, E.E.,Kraut, J.
      (1987) Biochemistry 26: 2674
    • Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis
      Filman, D.J.,Bolin, J.T.,Matthews, D.A.,Kraut, J.
      (1982) J.Biol.Chem. 257: 13663
    • Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding
      Matthews, D.A.,Alden, R.A.,Freer, S.T.,Xuong, N.-H.,Kraut, J.
      (1979) J.Biol.Chem. 254: 4144
    • Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate
      Matthews, D.A.,Alden, R.A.,Bolin, J.T.,Freer, S.T.,Hamlin, R.,Xuong, N.,Kraut, J.,Poe, M.,Williams, M.,Hoogsteen, K.
      (1977) Science 197: 452
    • Dihydrofolate Reductase. Purification and Characterization of the Enzyme from an Amethopterin-Resistant Mutant of Escherichia Coli
      Poe, M.,Greenfield, N.J.,Hirshfield, J.M.,Williams, M.N.,Hoogsteen, K.
      (1972) Biochemistry 11: 1023
    • Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
      Matthews, D.A.
      (1979) Biochemistry 18: 1602
    • Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph
      Volz, K.W.,Matthews, D.A.,Alden, R.A.,Freer, S.T.,Hansch, C.,Kaufman, B.T.,Kraut, J.
      (1982) J.Biol.Chem. 257: 2528
    • Dihydrofolate Reductase. The Amino Acid Sequence of the Enzyme from a Methotrexate-Resistant Mutant of Escherichia Coli
      Bennett, C.D.,Rodkey, J.A.,Sondey, J.M.,Hirschmann, R.
      (1978) Biochemistry 17: 1328


    Organizational Affiliation

    Department of Chemistry, University of California, San Diego, La Jolla 92093.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
159Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: folA (tmrA)
EC: 1.5.1.3
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABQ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.730α = 90.00
b = 68.730β = 90.00
c = 83.350γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other