4JAG

STRUCTURAL DETERMINATION OF THE A50T:S279G:S280K:V281K:K282E:H283N VARIANT OF CITRATE SYNTHASE FROM E. COLI COMPLEXED WITH oxaloacetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzyme-substrate complexes of allosteric citrate synthase: Evidence for a novel intermediate in substrate binding.

Duckworth, H.W.Nguyen, N.T.Gao, Y.Donald, L.J.Maurus, R.Ayed, A.Bruneau, B.Brayer, G.D.

(2013) Biochim.Biophys.Acta 1834: 2546-2553

  • DOI: 10.1016/j.bbapap.2013.07.019
  • Primary Citation of Related Structures:  4JAD, 4JAE, 4JAF

  • PubMed Abstract: 
  • The citrate synthase (CS) of Escherichia coli is an allosteric hexameric enzyme specifically inhibited by NADH. The crystal structure of wild type (WT) E. coli CS, determined by us previously, has no substrates bound, and part of the active site is i ...

    The citrate synthase (CS) of Escherichia coli is an allosteric hexameric enzyme specifically inhibited by NADH. The crystal structure of wild type (WT) E. coli CS, determined by us previously, has no substrates bound, and part of the active site is in a highly mobile region that is shifted from the position needed for catalysis. The CS of Acetobacter aceti has a similar structure, but has been successfully crystallized with bound substrates: both oxaloacetic acid (OAA) and an analog of acetyl coenzyme A (AcCoA). We engineered a variant of E. coli CS wherein five amino acids in the mobile region have been replaced by those in the A. aceti sequence. The purified enzyme shows unusual kinetics with a low affinity for both substrates. Although the crystal structure without ligands is very similar to that of the WT enzyme (except in the mutated region), complexes are formed with both substrates and the allosteric inhibitor NADH. The complex with OAA in the active site identifies a novel OAA-binding residue, Arg306, which has no functional counterpart in other known CS-OAA complexes. This structure may represent an intermediate in a multi-step substrate binding process where Arg306 changes roles from OAA binding to AcCoA binding. The second complex has the substrate analog, S-carboxymethyl-coenzyme A, in the allosteric NADH-binding site and the AcCoA site is not formed. Additional CS variants unable to bind adenylates at the allosteric site show that this second complex is not a factor in positive allosteric activation of AcCoA binding.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Citrate synthase
A, B
426Escherichia coli (strain K12)Gene Names: gltA (gluT, icdB)
EC: 2.3.3.16
Find proteins for P0ABH7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABH7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OAA
Query on OAA

Download SDF File 
Download CCD File 
A, B
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 165.152α = 90.00
b = 165.152β = 90.00
c = 158.841γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-18 
  • Released Date: 2013-07-17 
  • Deposition Author(s): Maurus, R., Brayer, G.D.
  • This entry supersedes: 3L99

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references
  • Version 1.2: 2013-10-23
    Type: Database references