1DR3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.140 

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

  • DOI: 10.1021/bi00078a008
  • Primary Citation of Related Structures:  
    1DR3, 1DR2

  • 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 complex with oxidized thionicotinamide adenine dinucleotide (thioNADP+) and in a ternary complex with thioNADP+ and biopterin ...

    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: 
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASEA189Gallus gallusMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
UniProt
Find proteins for P00378 (Gallus gallus)
Explore P00378 
Go to UniProtKB:  P00378
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAP (Subject of Investigation/LOI)
Query on TAP

Download Ideal Coordinates CCD File 
C [auth A]7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O16 P3 S
OJNFDOAQUXJWED-NNYOXOHSSA-N
 Ligand Interaction
HBI (Subject of Investigation/LOI)
Query on HBI

Download Ideal Coordinates CCD File 
D [auth A]7,8-DIHYDROBIOPTERIN
C9 H13 N5 O3
FEMXZDUTFRTWPE-DZSWIPIPSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.2α = 90
b = 48.31β = 124.8
c = 64.23γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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