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: 1.70 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:  
    3DFR, 4DFR

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

    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASEA162Lactobacillus caseiMutation(s): 0 
Gene Names: folAdhfR
EC: 1.5.1.3
Find proteins for P00381 (Lactobacillus casei)
Explore P00381 
Go to UniProtKB:  P00381
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
MTX
Query on MTX

Download CCD File 
A
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTXIC50:  0   nM  BindingDB
MTXKi:  0   nM  BindingDB
MTXIC50:  3   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.152 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.86α = 90
b = 71.86β = 90
c = 93.38γ = 120

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1982-10-21
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other, Structure summary