Homocitrate Synthase Lys4

Experimental Data Snapshot

  • Resolution: 2.24 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis.

Bulfer, S.L.Scott, E.M.Couture, J.F.Pillus, L.Trievel, R.C.

(2009) J Biol Chem 284: 35769-35780

  • DOI: https://doi.org/10.1074/jbc.M109.046821
  • Primary Citation of Related Structures:  
    3IVS, 3IVT, 3IVU

  • PubMed Abstract: 

    Homocitrate synthase (HCS) catalyzes the first and committed step in lysine biosynthesis in many fungi and certain Archaea and is a potential target for antifungal drugs. Here we report the crystal structure of the HCS apoenzyme from Schizosaccharomyces pombe and two distinct structures of the enzyme in complex with the substrate 2-oxoglutarate (2-OG). The structures reveal that HCS forms an intertwined homodimer stabilized by domain-swapping between the N- and C-terminal domains of each monomer. The N-terminal catalytic domain is composed of a TIM barrel fold in which 2-OG binds via hydrogen bonds and coordination to the active site divalent metal ion, whereas the C-terminal domain is composed of mixed alpha/beta topology. In the structures of the HCS apoenzyme and one of the 2-OG binary complexes, a lid motif from the C-terminal domain occludes the entrance to the active site of the neighboring monomer, whereas in the second 2-OG complex the lid is disordered, suggesting that it regulates substrate access to the active site through its apparent flexibility. Mutations of the active site residues involved in 2-OG binding or implicated in acid-base catalysis impair or abolish activity in vitro and in vivo. Together, these results yield new insights into the structure and catalytic mechanism of HCSs and furnish a platform for developing HCS-selective inhibitors.

  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homocitrate synthase, mitochondrial
A, B
423Schizosaccharomyces pombeMutation(s): 0 
Gene Names: lys4SPBC1105.02c
Find proteins for Q9Y823 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y823 
Go to UniProtKB:  Q9Y823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y823
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.24 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.995α = 90
b = 135.995β = 90
c = 122.124γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
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: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description