Crystal Structure of Threonine Synthase from Yeast

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 

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Structure and function of threonine synthase from yeast.

Garrido-Franco, M.Ehlert, S.Messerschmidt, A.Marinkovic, S.Huber, R.Laber, B.Bourenkov, G.P.Clausen, T.

(2002) J Biol Chem 277: 12396-12405

  • DOI: https://doi.org/10.1074/jbc.M108734200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Threonine synthase catalyzes the final step of threonine biosynthesis, the pyridoxal 5'-phosphate (PLP)-dependent conversion of O-phosphohomoserine into threonine and inorganic phosphate. Threonine is an essential nutrient for mammals, and its biosynthetic machinery is restricted to bacteria, plants, and fungi; therefore, threonine synthase represents an interesting pharmaceutical target. The crystal structure of threonine synthase from Saccharomyces cerevisiae has been solved at 2.7 A resolution using multiwavelength anomalous diffraction. The structure reveals a monomer as active unit, which is subdivided into three distinct domains: a small N-terminal domain, a PLP-binding domain that covalently anchors the cofactor and a so-called large domain, which contains the main of the protein body. All three domains show the typical open alpha/beta architecture. The cofactor is bound at the interface of all three domains, buried deeply within a wide canyon that penetrates the whole molecule. Based on structural alignments with related enzymes, an enzyme-substrate complex was modeled into the active site of yeast threonine synthase, which revealed essentials for substrate binding and catalysis. Furthermore, the comparison with related enzymes of the beta-family of PLP-dependent enzymes indicated structural determinants of the oligomeric state and thus rationalized for the first time how a PLP enzyme acts in monomeric form.

  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, am Klopferspitz 18A, Martinsried 82152, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine Synthase
A, B
514Saccharomyces cerevisiaeMutation(s): 7 
EC: (PDB Primary Data), (UniProt)
Find proteins for P16120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16120 
Go to UniProtKB:  P16120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16120
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.3α = 90
b = 51.6β = 99.6
c = 106.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Database references