Crystal structure of truncated alpha-Isopropylmalate Synthase from Neisseria meningitidis

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Removal of the C-terminal regulatory domain of alpha-isopropylmalate synthase disrupts functional substrate binding

Huisman, F.H.A.Koon, N.Bulloch, E.M.M.Baker, H.M.Baker, E.N.Squire, C.J.Parker, E.J.

(2012) Biochemistry 51: 2289-2297

  • DOI: https://doi.org/10.1021/bi201717j
  • Primary Citation of Related Structures:  
    3HPX, 3RMJ, 3U6W

  • PubMed Abstract: 

    α-Isopropylmalate synthase (α-IPMS) catalyzes the metal-dependent aldol reaction between α-ketoisovalerate (α-KIV) and acetyl-coenzyme A (AcCoA) to give α-isopropylmalate (α-IPM). This reaction is the first committed step in the biosynthesis of leucine in bacteria. α-IPMS is homodimeric, with monomers consisting of (β/α)(8) barrel catalytic domains fused to a C-terminal regulatory domain, responsible for binding leucine and providing feedback regulation for leucine biosynthesis. In these studies, we demonstrate that removal of the regulatory domain from the α-IPMS enzymes of both Neisseria meningitidis (NmeIPMS) and Mycobacterium tuberculosis (MtuIPMS) results in enzymes that are unable to catalyze the formation of α-IPM, although truncated NmeIPMS was still able to slowly hydrolyze AcCoA. The lack of catalytic activity of these truncation variants was confirmed by complementation studies with Escherichia coli cells lacking the α-IPMS gene, where transformation with the plasmids encoding the truncated α-IPMS enzymes was not able to rescue α-IPMS activity. X-ray crystal structures of both truncation variants reveal that both proteins are dimeric and that the catalytic sites of the proteins are intact, although the divalent metal ion that is thought to be responsible for activating substrate α-KIV is displaced slightly relative to its position in the substrate-bound, wild-type structure. Isothermal titration calorimetry and WaterLOGSY nuclear magnetic resonance experiments demonstrate that although these truncation variants are not able to catalyze the reaction between α-KIV and AcCoA, they are still able to bind the substrate α-KIV. It is proposed that the regulatory domain is crucial for ensuring protein dynamics necessary for competent catalysis.

  • Organizational Affiliation

    Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-isopropylmalate synthase
A, B
370Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: leuANMB1070
Find proteins for Q9JZG1 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZG1 
Go to UniProtKB:  Q9JZG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZG1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
C3 H8 O3
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.296α = 90
b = 103.581β = 90
c = 129.937γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description