2P4T

Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode.

Divya, N.Grifith, E.Narayana, N.

(2007) Protein Sci. 16: 1063-1068

  • DOI: 10.1110/ps.062740907

  • PubMed Abstract: 
  • Plasmid-encoded bacterial R67 dihydrofolate reductase (DHFR) is a NADPH-dependent enzyme unrelated to chromosomal DHFR in amino acid sequence and structure. R67 DHFR is insensitive to the bacterial drug trimethoprim in contrast to chromosomal DHFR. T ...

    Plasmid-encoded bacterial R67 dihydrofolate reductase (DHFR) is a NADPH-dependent enzyme unrelated to chromosomal DHFR in amino acid sequence and structure. R67 DHFR is insensitive to the bacterial drug trimethoprim in contrast to chromosomal DHFR. The crystal structure of Q67H mutant of R67 DHFR bound to NADP(+) has been determined at 1.15 angstroms resolution. The cofactor assumes an extended conformation with the nicotinamide ring bound near the center of the active site pore, the ribose and pyrophosphate group (PP(i)) extending toward the outer pore. The ribonicotinamide exhibits anti conformation as in chromosomal DHFR complexes. The relative orientation between the PP(i) and the nicotinamide ribose differs from that observed in chromosomal DHFR-NADP(+) complexes. The coenzyme displays symmetrical binding mode with several water-mediated hydrogen bonds with the protein besides ionic, stacking, and van der Waals interactions. The structure provides a molecular basis for the observed stoichiometry and cooperativity in ligand binding. The ternary model based on the present structure and the previous R67 DHFR-folate complex provides insight into the catalytic mechanism and indicates that the relative orientation of the reactants in plasmid DHFR is different from that seen in chromosomal DHFRs.


    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.,Xuong, N.
      (1995) Nat.Struct.Mol.Biol. 2: 1018
    • A glutamine 67-->histidine mutation in homotetrameric R67 dihydrofolate reductase results in four mutations per single active site pore and causes substantial substrate and cofactor inhibition
      Park, H.,Bradrick, T.D.,Howell, E.E.
      (1997) Protein Eng. 10: 1415
    • High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site
      Narayana, N.
      (2006) Acta Crystallogr.,Sect.D 62: 695


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase type 2
A
62Escherichia coliMutation(s): 1 
EC: 1.5.1.3
Find proteins for P00383 (Escherichia coli)
Go to UniProtKB:  P00383
Small Molecules
Ligands 1 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKd: 27 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.460α = 90.00
b = 67.460β = 90.00
c = 52.860γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
TNTrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-03-13
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance