Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.55 kDa 
• Atom Count: 1,639 
• Modelled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

 3DFR

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

• PDB DOI:  https://doi.org/10.2210/pdb3DFR/pdb
• Entry: 3DFR supersedes: 1DFR

• Classification: OXIDOREDUCTASE
• Organism(s): Lacticaseibacillus casei
• Mutation(s): No 


• Deposited: 1982-06-25 Released: 1982-10-21 
• Deposition Author(s): Filman, D.J., Matthews, D.A., Bolin, J.T., Kraut, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.152 

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

• PubMed: 6815178 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A	162	Lacticaseibacillus casei	Mutation(s): 0  Gene Names: folA, dhfR EC: 1.5.1.3
UniProt
Find proteins for P00381 (Lactobacillus casei) Explore P00381  Go to UniProtKB:  P00381

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
MTX	C [auth A]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTX	BindingDB:  3DFR	Ki: 4.00e-3 (nM) from 1 assay(s)
		IC50: min: 1.3, max: 55 (nM) from 17 assay(s)
	Binding MOAD:  3DFR	IC50: 3 (nM) from 1 assay(s)

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 = 71.86	α = 90
b = 71.86	β = 90
c = 93.38	γ = 120

Structure Validation

Entry History 

Deposition Data

• Released Date: 1982-10-21 
Deposition Author(s): Filman, D.J., Matthews, D.A., Bolin, J.T., Kraut, J.
• This entry supersedes: 1DFR

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