1UIM

Crystal Structure of Threonine Synthase from Thermus Thermophilus HB8, Orthorhombic Crystal Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Threonine Synthase from Thermus thermophilus HB8: Conformational change, substrate recognition, and mechanism.

Omi, R.Masaru, G.Miyahara, I.Mizuguchi, H.Hayashi, H.Kagamiyama, H.Hirotsu, K.

(2003) J Biol Chem 278: 46035-46045

  • DOI: https://doi.org/10.1074/jbc.M308065200
  • Primary Citation of Related Structures:  
    1UIM, 1UIN, 1V7C

  • PubMed Abstract: 

    Threonine synthase, which is a PLP-dependent enzyme, catalyzes the beta,gamma-replacement reaction of l-homoserine phosphate to yield threonine and inorganic phosphate. The three-dimensional structures of the enzyme from Thermus thermophilus HB8 in its unliganded form and complexed with the substrate analogue 2-amino-5-phosphonopentanoic acid have been determined at 2.15 and 2.0 A resolution, respectively. The complexed form, assigned as an enamine, uncovered the interactions of the cofactor-analogue conjugate with the active site residues. The binding of the substrate analogue induces a large conformational change at the domain level. The small domain rotates by about 25 degrees and approaches the large domain to close the active site. The complicated catalytic process of the enzyme has been elucidated based on the complex structure to reveal the stereochemistry of the reaction and to present the released inorganic phosphate as a possible catalyst to carry a proton to the Cgamma atom of the substrate.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine Synthase
A, B
351Thermus thermophilusMutation(s): 0 
Gene Names: HB8
EC: 4.2.3.1
UniProt
Find proteins for P83823 (Thermus thermophilus)
Explore P83823 
Go to UniProtKB:  P83823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83823
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.068α = 90
b = 83.271β = 90
c = 123.504γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations