2GQV

High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.099 
  • R-Value Observed: 0.105 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D(2)-symmetric active site.

Narayana, N.

(2006) Acta Crystallogr D Biol Crystallogr 62: 695-706

  • DOI: 10.1107/S0907444906014764
  • Primary Citation of Related Structures:  
    2GQV

  • PubMed Abstract: 
  • R67 plasmid-encoded dihydrofolate reductase (R67 DHFR) is an NADPH-dependent homotetrameric enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. The amino-acid sequence and molecular architecture of R67 DHFR and its inhibitory properties toward folate analogues are different from those of chromosomal DHFR ...

    R67 plasmid-encoded dihydrofolate reductase (R67 DHFR) is an NADPH-dependent homotetrameric enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. The amino-acid sequence and molecular architecture of R67 DHFR and its inhibitory properties toward folate analogues are different from those of chromosomal DHFR. Here, the crystal structure of R67 DHFR refined using 1.1 A resolution data is presented. Blocked full-matrix least-squares refinement without restraints resulted in a final R factor of 11.4%. The anisotropic atomic displacement parameters analyzed by Rosenfield matrices and translation-libration-screw validation suggested four quasi-rigid domains. A total of ten Calpha-H...O hydrogen bonds were identified between the beta-strands. There is reasonable structural evidence that His62 is not protonated in the tetramer, which is in accord with previous pH-profile studies. The side chain of Gln67 that protrudes into the active site exhibits dual conformation, a feature noticed for the first time owing to the availability of atomic resolution data. The R67 DHFR active site is unique: it has D2 symmetry and is a large active site with a pentagonal network of water molecules and exposure of backbone atoms to solvent; the central pore is favorable for planar ring-stacking interactions. The geometrical shape, overall symmetry, local asymmetry and waters appear to dominate the binding of ligands, catalysis and inhibition.


    Related Citations: 
    • A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
      Narayana, N., Matthews, D.A., Howell, E.E., Nguyen-huu, X.
      (1995) Nat Struct Biol 2: 1018
    • Crystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67.
      Matthews, D.A., Smith, S.L., Baccanari, D.P., Burchall, J.J., Oatley, S.J., Kraut, J.
      (1986) Biochemistry 25: 4194

    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA. nxn17@case.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrofolate reductase type 2A62Escherichia coliMutation(s): 0 
EC: 1.5.1.3
UniProt
Find proteins for P00383 (Escherichia coli)
Explore P00383 
Go to UniProtKB:  P00383
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00383
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.099 
  • R-Value Observed: 0.105 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.05α = 90
b = 68.05β = 90
c = 52.244γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-04-22 
  • Released Date: 2007-04-24 
  • Deposition Author(s): Narayana, N.

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description