1DR1

2.2 ANGSTROMS CRYSTAL STRUCTURE OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADP+ AND BIOPTERIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of chicken liver dihydrofolate reductase complexed with NADP+ and biopterin.

McTigue, M.A.Davies 2nd., J.F.Kaufman, B.T.Kraut, J.

(1992) Biochemistry 31: 7264-7273


  • PubMed Abstract: 
  • The 2.2-A crystal structure of chicken liver dihydrofolate reductase (EC 1.5.1.3, DHFR) has been solved as a ternary complex with NADP+ and biopterin (a poor substrate). The space group and unit cell are isomorphous with the previously reported struc ...

    The 2.2-A crystal structure of chicken liver dihydrofolate reductase (EC 1.5.1.3, DHFR) has been solved as a ternary complex with NADP+ and biopterin (a poor substrate). The space group and unit cell are isomorphous with the previously reported structure of chicken liver DHFR complexed with NADPH and phenyltriazine [Volz, K. W., Matthews, D. A., Alden, R. A., Freer, S. T., Hansch, C., Kaufman, B. T., & Kraut, J. (1982) J. Biol. Chem. 257, 2528-2536]. The structure contains an ordered water molecule hydrogen-bonded to both hydroxyls of the biopterin dihydroxypropyl group as well as to O4 and N5 of the biopterin pteridine ring. This water molecule, not observed in previously determined DHFR structures, is positioned to complete a proposed route for proton transfer from the side-chain carboxylate of E30 to N5 of the pteridine ring. Protonation of N5 is believed to occur during the reduction of dihydropteridine substrates. The positions of the NADP+ nicotinamide and biopterin pteridine rings are quite similar to the nicotinamide and pteridine ring positions in the Escherichia coli DHFR.NADP+.folate complex [Bystroff, C., Oatley, S. J., & Kraut, J. (1990) Biochemistry 29, 3263-3277], suggesting that the reduction of biopterin and the reduction of folate occur via similar mechanisms, that the binding geometry of the nicotinamide and pteridine rings is conserved between DHFR species, and that the p-aminobenzoylglutamate moiety of folate is not required for correct positioning of the pteridine ring in ground-state ternary complexes. Instead, binding of the p-aminobenzoylglutamate moiety of folate may induce the side chain of residue 31 (tyrosine or phenylalanine) in vertebrate DHFRs to adopt a conformation in which the opening to the pteridine binding site is too narrow to allow the substrate to diffuse away rapidly. A reverse conformational change of residue 31 is proposed to be required for tetrahydrofolate release.


    Related Citations: 
    • Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate
      Davies II, J.F.,Delcamp, T.J.,Prendergast, N.J.,Ashford, V.A.,Freisheim, J.H.,Kraut, J.
      (1990) Biochemistry 29: 9467
    • 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
    • Primary Structure of Chicken Liver Dihydrofolate Reductase
      Kumar, A.A.,Blankenship, D.T.,Kaufman, B.T.,Freisheim, J.H.
      (1980) Biochemistry 19: 667
    • Refined Crystal Structure of Escherichia Coli and Chicken Liver Dihydrofolate Reductase Containing Bound Trimethoprim
      Matthews, D.A.,Bolin, J.T.,Burridge, J.M.,Filman, D.J.,Volz, K.W.,Kaufman, B.T.,Beddell, C.R.,Champness, J.N.,Stammers, D.K.,Kraut, J.
      (1985) J.Biol.Chem. 260: 381
    • Dihydrofolate Reductase, the Stereochemistry of Inhibitor Selectivity
      Matthews, D.A.,Bolin, J.T.,Burridge, J.M.,Filman, D.J.,Volz, K.W.,Kraut, J.
      (1985) J.Biol.Chem. 260: 392


    Organizational Affiliation

    Department of Chemistry, University of California, San Diego, La Jolla 92093-0317.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
189Gallus gallusGene Names: DHFR
EC: 1.5.1.3
Find proteins for P00378 (Gallus gallus)
Go to Gene View: DHFR
Go to UniProtKB:  P00378
Small Molecules
Ligands 3 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
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HBI
Query on HBI

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Download CCD File 
A
7,8-DIHYDROBIOPTERIN
C9 H13 N5 O3
FEMXZDUTFRTWPE-DZSWIPIPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.440α = 90.00
b = 48.310β = 125.10
c = 64.260γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other