1DR2

2.3 ANGSTROMS CRYSTAL STRUCTURE OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXED WITH THIONADP+ AND BIOPTERIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of chicken liver dihydrofolate reductase: binary thioNADP+ and ternary thioNADP+.biopterin complexes.

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

(1993) Biochemistry 32: 6855-6862

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The role of the 3'-carboxamide substituent of NADPH in the reduction of pteridine substrates as catalyzed by dihydrofolate reductase (EC 1.5.1.3, DHFR) has been investigated by determining crystal structures at 2.3 A of chicken liver DHFR in a binary ...

    The role of the 3'-carboxamide substituent of NADPH in the reduction of pteridine substrates as catalyzed by dihydrofolate reductase (EC 1.5.1.3, DHFR) has been investigated by determining crystal structures at 2.3 A of chicken liver DHFR in a binary complex with oxidized thionicotinamide adenine dinucleotide (thioNADP+) and in a ternary complex with thioNADP+ and biopterin. These structures are isomorphous with those previously reported for chicken liver DHFR [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]. ThioNADPH, which has a 3'-carbothioamide substituent in place of a 3'-carboxamide, functions very poorly as a coenzyme for DHFR [Williams, T. J., Lee, T. K., & Dunlap, R. B. (1977) Arch, Biochem. Biophys. 181, 569-579; Stone, S. R., Mark, A., & Morrison, J. F. (1984) Biochemistry 23, 4340-4346]. Comparisons show that, while NADP+ and NADPH bind to DHFR with the pyridine ring and 3'-carboxamide coplanar, the thioamide group is twisted by 23 degrees from the pyridine plane in both the binary and ternary complexes. This twist appears to be due to steric conflict between the thioamide sulfur atom and both the pyridine ring at C4 and the adjacent protein backbone at Ala-9. It results in an unfavorably close contact between the sulfur and the biopterin pteridine ring (0.9 A less than the van der Waals separation) which, on the basis of the refined structure, greatly destabilizes the binding of biopterin.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • 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
    • 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
    • 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
    • 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


    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 gallusMutation(s): 0 
Gene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

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Download CCD File 
A
7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
TATP
C21 H28 N7 O16 P3 S
OJNFDOAQUXJWED-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.020α = 90.00
b = 48.240β = 124.63
c = 64.110γ = 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