PDBsum entry 1uim

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Lyase PDB id
Protein chains
350 a.a. *
PLP ×2
Waters ×283
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of threonine synthase from thermus thermop orthorhombic crystal form
Structure: Threonine synthase. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.15Å     R-factor:   0.210     R-free:   0.251
Authors: R.Omi,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Omi et al. (2003). Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism. J Biol Chem, 278, 46035-46045. PubMed id: 12952961 DOI: 10.1074/jbc.M308065200
17-Jul-03     Release date:   18-Nov-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P83823  (P83823_THETH) -  Threonine synthase
351 a.a.
350 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Threonine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Threonine Biosynthesis
      Reaction: O-phospho-L-homoserine + H2O = L-threonine + phosphate
Bound ligand (Het Group name = PLP)
matches with 58.00% similarity
+ H(2)O
= L-threonine
+ phosphate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular amino acid metabolic process   3 terms 
  Biochemical function     lyase activity     3 terms  


DOI no: 10.1074/jbc.M308065200 J Biol Chem 278:46035-46045 (2003)
PubMed id: 12952961  
Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism.
R.Omi, M.Goto, I.Miyahara, H.Mizuguchi, H.Hayashi, H.Kagamiyama, K.Hirotsu.
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.
  Selected figure(s)  
Figure 6.
FIG. 6. Schematic diagram showing hydrogen bond and salt bridge interactions of the active site residues. The unliganded tThrS (A) and tThrS·AP5 complex (B). Putative interactions are shown by dotted lines if the acceptor and donor are less than 3.3 Å apart.
Figure 9.
FIG. 9. The proposed reaction mechanism of ThrS with the substrate, HSerP. A, Michaelis complex; B, external aldimine; C, carbanion intermediate; D, ketimine; E, enamine; F, , -unsaturated ketimine; G, , -unsaturated aldimine; H, external aldimine between PLP and threonine.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 46035-46045) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19761441 D.E.Graham, S.M.Taylor, R.Z.Wolf, and S.C.Namboori (2009).
Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase.
  Biochem J, 424, 467-478.  
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
19155267 T.Yamauchi, M.Goto, H.Y.Wu, T.Uo, T.Yoshimura, H.Mihara, T.Kurihara, I.Miyahara, K.Hirotsu, and N.Esaki (2009).
Serine racemase with catalytically active lysinoalanyl residue.
  J Biochem, 145, 421-424.
PDB code: 2zpu
16525757 R.A.Azevedo, M.Lancien, and P.J.Lea (2006).
The aspartic acid metabolic pathway, an exciting and essential pathway in plants.
  Amino Acids, 30, 143-162.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.