Crystal structure of homocitrate synthase from Thermus thermophilus complexed with Lys

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus

Okada, T.Tomita, T.Wulandari, A.P.Kuzuyama, T.Nishiyama, M.

(2010) J Biol Chem 285: 4195-4205

  • DOI: https://doi.org/10.1074/jbc.M109.086330
  • Primary Citation of Related Structures:  
    2ZTJ, 2ZTK, 2ZYF, 3A9I

  • PubMed Abstract: 

    Homocitrate synthase (HCS) catalyzes aldol-type condensation of acetyl coenzyme A (acetyl-CoA) and alpha-ketoglutarate (alpha-KG) to synthesize homocitrate (HC), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. As known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, HCS is regulated via feedback inhibition by the end product, lysine. Here, we determined the crystal structures of HCS from Thermus thermophilus complexed with alpha-KG, HC, or lysine. In the HC complex, the C1-carboxyl group of HC, which is derived from acetyl-CoA, is hydrogen-bonded with His-292* from another subunit (indicated by the asterisk), indicating direct involvement of this residue in the catalytic mechanism of HCS. The crystal structure of HCS complexed with lysine showed that lysine is bound to the active site with rearrangement of amino acid residues in the substrate-binding site, which accounts for the competitive inhibition by lysine with alpha-KG. Comparison between the structures suggests that His-72, which is conserved in lysine-sensitive HCSs and binds the C5-carboxyl group of alpha-KG, serves as a switch for the conformational change. Replacement of His-72 by leucine made HCS resistant to lysine inhibition, demonstrating the regulatory role of this conserved residue.

  • Organizational Affiliation

    From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homocitrate synthase376Thermus thermophilus HB27Mutation(s): 0 
Find proteins for O87198 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore O87198 
Go to UniProtKB:  O87198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87198
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LYS PDBBind:  3A9I Ki: 7.07e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.281α = 90
b = 96.025β = 90
c = 77.082γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2012-01-25
    Changes: Database references, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description