Three Dimensional Structure Analysis Of The Variant R109L NADH Complex of Type II Citrate Synthase From E. Coli

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.162 

Starting Model: experimental
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Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli.

Stokell, D.J.Donald, L.J.Maurus, R.Nguyen, N.T.Sadler, G.Choudhary, K.Hultin, P.G.Brayer, G.D.Duckworth, H.W.

(2003) J Biol Chem 278: 35435-35443

  • DOI: https://doi.org/10.1074/jbc.M302786200
  • Primary Citation of Related Structures:  
    1OWB, 1OWC

  • PubMed Abstract: 

    The citrate synthase of Escherichia coli is an example of a Type II citrate synthase, a hexamer that is subject to allosteric inhibition by NADH. In previous crystallographic work, we defined the NADH binding sites, identifying nine amino acids whose side chains were proposed to make hydrogen bonds with the NADH molecule. Here, we describe the functional properties of nine sequence variants, in which these have been replaced by nonbonding residues. All of the variants show some changes in NADH binding and inhibition and small but significant changes in kinetic parameters for catalysis. In three cases, Y145A, R163L, and K167A, NADH inhibition has become extremely weak. We have used nanospray/time-of-flight mass spectrometry, under non-denaturing conditions, to show that two of these, R163L and K167A, do not form hexamers in response to NADH binding, unlike the wild type enzyme. One variant, R109L, shows tighter NADH binding. We have crystallized this variant and determined its structure, with and without bound NADH. Unexpectedly, the greatest structural changes in the R109L variant are in two regions outside the NADH binding site, both of which, in wild type citrate synthase, have unusually high mobilities as measured by crystallographic thermal factors. In the R109L variant, both regions (residues 260 -311 and 316-342) are much less mobile and have rearranged significantly. We argue that these two regions are elements in the path of communication between the NADH binding sites and the active sites and are centrally involved in the regulatory conformational change in E. coli citrate synthase.

  • Organizational Affiliation

    Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase
A, B
427Escherichia coliMutation(s): 1 
Find proteins for P0ABH7 (Escherichia coli (strain K12))
Explore P0ABH7 
Go to UniProtKB:  P0ABH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABH7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.162 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.001α = 90
b = 165.001β = 90
c = 157.774γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description