1RX5

DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEXED WITH 5,10-DIDEAZATETRAHYDROFOLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.

Sawaya, M.R.Kraut, J.

(1997) Biochemistry 36: 586-603

  • DOI: 10.1021/bi962337c
  • Primary Citation of Related Structures:  
  • Also Cited By: 3QL3

  • PubMed Abstract: 
  • The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Is ...

    The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Isomorphous crystal structures analogous to these five intermediates and to the transition state (as represented by the methotrexate-NADPH complex) have been used to assemble a 2.1 A resolution movie depicting loop and subdomain movements during the catalytic cycle (see Supporting Information). The structures suggest that the M20 loop is predominantly closed over the reactants in the holoenzyme, Michaelis, and transition state complexes. But, during the remainder of the cycle, when nicotinamide is not bound, the loop occludes (protrudes into) the nicotinamide-ribose binding pocket. Upon changing from the closed to the occluded conformation, the central portion of the loop rearranges from beta-sheet to 3(10) helix. The change may occur by way of an irregularly structured open loop conformation, which could transiently admit a water molecule into position to protonate N5 of dihydrofolate. From the Michaelis to the transition state analogue complex, rotation between two halves of ecDHFR, the adenosine binding subdomain and loop subdomain, closes the (p-aminobenzoyl)glutamate (pABG) binding crevice by approximately 0.5 A. Resulting enhancement of contacts with the pABG moiety may stabilize puckering at C6 of the pteridine ring in the transition state. The subdomain rotation is further adjusted by cofactor-induced movements (approximately 0.5 A) of helices B and C, producing a larger pABG cleft in the THF.NADPH analogue complex than in the THF analogue complex. Such movements may explain how THF release is assisted by NADPH binding. Subdomain rotation is not observed in vertebrate DHFR structures, but an analogous loop movement (residues 59-70) appears to similarly adjust the pABG cleft width, suggesting that these movements are important for catalysis. Loop movement, also unobserved in vertebrate DHFR structures, may preferentially weaken NADP+ vs NADPH binding in ecDHFR, an evolutionary adaptation to reduce product inhibition in the NADP+ rich environment of prokaryotes.


    Related Citations: 
    • Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding
      Bystroff, C.,Kraut, J.
      (1991) Biochemistry 30: 2227
    • Isomorphous Crystal Structures of Escherichia Coli Dihydrofolate Reductase Complexed with Folate, 5-Deazafolate, and 5,10-Dideazatetrahydrofolate: Mechanistic Implications
      Reyes, V.M.,Sawaya, M.R.,Brown, K.A.,Kraut, J.
      (1995) Biochemistry 34: 2710
    • Crystal Structures of Escherichia Coli Dihydrofolate Reductase: The Nadp+ Holoenzyme and the Folate.Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State
      Bystroff, C.,Oatley, S.J.,Kraut, J.
      (1990) Biochemistry 29: 3263


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA.




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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.808α = 90.00
b = 44.761β = 90.00
c = 100.826γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
UCSDdata scaling
TNTphasing
UCSDdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-09-19 
  • Released Date: 1997-01-11 
  • Deposition Author(s): Sawaya, M.R.

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance