4PDJ

Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.994 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.599 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography.

Wan, Q.Bennett, B.C.Wilson, M.A.Kovalevsky, A.Langan, P.Howell, E.E.Dealwis, C.

(2014) Proc.Natl.Acad.Sci.USA 111: 18225-18230

  • DOI: 10.1073/pnas.1415856111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation sta ...

    Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to a lack of consensus regarding the catalytic mechanism involved. To resolve this ambiguity, we conducted neutron and ultrahigh-resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of Escherichia coli DHFR with folate and NADP(+). The neutron data were collected to 2.0-Å resolution using a 3.6-mm(3) crystal with the quasi-Laue technique. The structure reveals that the N3 atom of folate is protonated, whereas Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer owing to protonation of the N3 atom, suggesting that tautomerization is unnecessary for catalysis. In the 1.05-Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa value of the N5 atom of DHF by Asp27, and protonation of N5 by water that gains access to the active site through fluctuation of the Met20 side chain even though the Met20 loop is closed.


    Organizational Affiliation

    Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Disease, Yangzhou 225001, People's Republic of China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, People's Republic of China; Department of Biochemistry, College of Medicine, Yangzhou University, Yangzhou 225001, People's Republic of China;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
159Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: folA (tmrA)
EC: 1.5.1.3
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABQ4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DHF
Query on DHF

Download SDF File 
Download CCD File 
A
DIHYDROFOLIC ACID
C19 H21 N7 O6
OZRNSSUDZOLUSN-LBPRGKRZSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.994 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.599 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.293α = 90.00
b = 45.625β = 90.00
c = 98.974γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data processing
LAUEGENdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
SCALAdata reduction
SCALAdata scaling
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesFWP ERKP752
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM071939
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM092999
Yangzhou UniversityChina2013CXJ083
State Education MinistryChina--

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Data collection
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy