5CC9

L28F E.coli dihydrofolate reductase complexed with 5,10-dideazatetrahydrofolate and oxidized nicotinamide adenine dinucleotide phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.199 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway.

Oyen, D.Fenwick, R.B.Stanfield, R.L.Dyson, H.J.Wright, P.E.

(2015) J.Am.Chem.Soc. 137: 9459-9468

  • DOI: 10.1021/jacs.5b05707
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme dihydrofolate reductase (DHFR, E) from Escherichia coli is a paradigm for the role of protein dynamics in enzyme catalysis. Previous studies have shown that the enzyme progresses through the kinetic cycle by modulating the dynamic conforma ...

    The enzyme dihydrofolate reductase (DHFR, E) from Escherichia coli is a paradigm for the role of protein dynamics in enzyme catalysis. Previous studies have shown that the enzyme progresses through the kinetic cycle by modulating the dynamic conformational landscape in the presence of substrate dihydrofolate (DHF), product tetrahydrofolate (THF), and cofactor (NADPH or NADP(+)). This study focuses on the quantitative description of the relationship between protein fluctuations and product release, the rate-limiting step of DHFR catalysis. NMR relaxation dispersion measurements of millisecond time scale motions for the E:THF:NADP(+) and E:THF:NADPH complexes of wild-type and the Leu28Phe (L28F) point mutant reveal conformational exchange between an occluded ground state and a low population of a closed state. The backbone structures of the occluded ground states of the wild-type and mutant proteins are very similar, but the rates of exchange with the closed excited states are very different. Integrated analysis of relaxation dispersion data and THF dissociation rates measured by stopped-flow spectroscopy shows that product release can occur by two pathways. The intrinsic pathway consists of spontaneous product dissociation and occurs for all THF-bound complexes of DHFR. The allosteric pathway features cofactor-assisted product release from the closed excited state and is utilized only in the E:THF:NADPH complexes. The L28F mutation alters the partitioning between the pathways and results in increased flux through the intrinsic pathway relative to the wild-type enzyme. This repartitioning could represent a general mechanism to explain changes in product release rates in other E. coli DHFR mutants.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
159Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: folA (tmrA)
EC: 1.5.1.3
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABQ4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDF
Query on DDF

Download SDF File 
Download CCD File 
A
5,10-DIDEAZATETRAHYDROFOLIC ACID
C21 H25 N5 O6
ZUQBAQVRAURMCL-DOMZBBRYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.199 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.536α = 90.00
b = 58.245β = 90.00
c = 79.377γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-01 
  • Released Date: 2015-08-05 
  • Deposition Author(s): Oyen, D., Wright, P.E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM75995

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations