1DHI

LONG-RANGE STRUCTURAL EFFECTS IN A SECOND-SITE REVERTANT OF A MUTANT DIHYDROFOLATE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Long-range structural effects in a second-site revertant of a mutant dihydrofolate reductase.

Brown, K.A.Howell, E.E.Kraut, J.

(1993) Proc Natl Acad Sci U S A 90: 11753-11756

  • DOI: 10.1073/pnas.90.24.11753
  • Primary Citation of Related Structures:  
    1DHJ, 1DHI

  • PubMed Abstract: 
  • X-ray crystal structures have been determined for a second-site revertant (Asp-27-->Ser, Phe-137-->Ser; D27S/F137S) and both component single-site mutants of Escherichia coli dihydrofolate reductase. The primary D27S mutation, located in the substrate binding pocket, greatly reduces catalytic activity as compared to the wild-type enzyme ...

    X-ray crystal structures have been determined for a second-site revertant (Asp-27-->Ser, Phe-137-->Ser; D27S/F137S) and both component single-site mutants of Escherichia coli dihydrofolate reductase. The primary D27S mutation, located in the substrate binding pocket, greatly reduces catalytic activity as compared to the wild-type enzyme. The additional F137S mutation, which partially restores catalytic activity, is located on the surface of the molecule, well outside of the catalytic center and approximately 15 A from residue 27. Comparison of kinetic data for the single-site F137S mutant, specifically constructed as a control, and for the double-mutant enzymes indicates that the effects of the F137S and D27S mutations on catalysis are nonadditive. This result suggests that the second-site mutation might mediate its effects through a structural perturbation propagated along the polypeptide backbone. To investigate the mechanism by which the F137S substitution elevates the catalytic activity of D27S we have determined the structure of the D27S/F137S double mutant. We also present a rerefined structure for the original D27S mutant and a preliminary structural interpretation for the F137S single-site mutant. We find that while either single mutant shows little more than a simple side-chain substitution, the double mutant undergoes an extended structural perturbation, which is propagated between these two widely separated sites via the helix alpha B.


    Related Citations: 
    • How Do Mutation at Phenylalanine-153 and Isoleucine-155 Partially Suppress the Effects of the Aspartate-27-> Serine Mutation in Escherichia Coli Dihydrofolate Reductase
      Dion, A., Linn, C.E., Bradrick, T.D., Georghiou, S., Howell, E.E.
      (1993) Biochemistry 32: 3479
    • Role of Aspartate 27 of Dihydrofolate Reductase from Escherichia Coli in Interconversion of Active and Inactive Enzyme Conformers and the Binding of Nadph
      Appleman, J.R., Howell, E.E., Kraut, J., Blakely, R.L.
      (1990) J Biol Chem 265: 5579
    • A Second-Site Mutation at Phenylalanine-137 that Increases Catalytic Efficiency in the Mutant Aspartate-27-> Serine Escherichia Coli Dihydrofolate Reductase
      Howell, E.E., Booth, C., Farnum, M., Kraut, J., Warren, M.S.
      (1990) Biochemistry 29: 8561
    • Dihydrofolate Reductase from Escherichia Coli: Probing the Role of Aspartate-27 and Phenylalanine-137 in Enzyme Conformation and the Binding of Nadph
      Dunn, S.M., Lanigan, T.M., Howell, E.E.
      (1990) Biochemistry 29: 8569
    • Functional Role of Aspartic Acid-27 in Dihydrofolate Reductase Revealed by Mutagenesis
      Howell, E.E., Villafranca, J.E., Waren, M.S., Oatley, S.J., Kraut, J.
      (1986) Science 231: 1123
    • Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
      Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., Kraut, J.
      (1982) Biochemistry 257: 13650
    • Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASEA, B159Escherichia coliMutation(s): 0 
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTXIC50:  6.599999904632568   nM  BindingDB
MTXEC50:  1   nM  BindingDB
MTXKd:  55   nM  Binding MOAD
MTXIC50:  3   nM  BindingDB
MTXKd :  55   nM  PDBBind
MTXIC50:  8.800000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.155 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.19α = 90
b = 93.19β = 90
c = 73.92γ = 120
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    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