3DFR

CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A 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: 13650-13662

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures hav ...

    X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.


    Related Citations: 
    • 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 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 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
    • Properties of Thymidylate Synthetase from Dichloromethotrexate-Resistant Lactobacillus Casei
      Crusberg, T.C.,Leary, R.,Kisliuk, R.L.
      (1970) J.Biol.Chem. 245: 5292
    • 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
    • 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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
162Lactobacillus caseiMutation(s): 0 
Gene Names: folA (dhfR)
EC: 1.5.1.3
Find proteins for P00381 (Lactobacillus casei)
Go to UniProtKB:  P00381
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX

Download SDF File 
Download CCD File 
A
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTXIC50: 1.3 - 55 nM (98) BINDINGDB
MTXKi: 0 nM (98) BINDINGDB
MTXIC50: 3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.152 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 71.860α = 90.00
b = 71.860β = 90.00
c = 93.380γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1982-10-21
    Type: Initial release
  • Version 1.1: 2008-03-03
    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