7DFR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state.

Bystroff, C.Oatley, S.J.Kraut, J.

(1990) Biochemistry 29: 3263-3277

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of dihydrofolate reductase (EC 1.5.1.3) from Escherichia coli has been solved as the binary complex with NADP+ (the holoenzyme) and as the ternary complex with NADP+ and folate. The Bragg law resolutions of the structures are 2. ...

    The crystal structure of dihydrofolate reductase (EC 1.5.1.3) from Escherichia coli has been solved as the binary complex with NADP+ (the holoenzyme) and as the ternary complex with NADP+ and folate. The Bragg law resolutions of the structures are 2.4 and 2.5 A, respectively. The new crystal forms are nonisomorphous with each other and with the methotrexate binary complex reported earlier [Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., & Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662]. In general, NADP+ and folate binding conform to predictions, but the nicotinamide moiety of NADP+ is disordered in the holoenzyme and ordered in the ternary complex. A mobile loop (residues 16-20) involved in binding the nicotinamide is also disordered in the holoenzyme. We report a detailed analysis of the binding interactions for both ligands, paying special attention to several apparently strained interactions that may favor the transition state for hydride transfer. Hypothetical models are presented for the binding of 7,8-dihydrofolate in the Michaelis complex and for the transition-state complex.


    Related Citations: 
    • 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 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
    • 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 Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding
      Bystroff, C.,Kraut, J.
      () TO BE PUBLISHED --: --
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
FOL
Query on FOL

Download SDF File 
Download CCD File 
A
FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.207α = 90.00
b = 62.207β = 90.00
c = 105.525γ = 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, Structure summary