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PDBsum entry 1kl7

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1kl7
Jmol
Contents
Protein chains
509 a.a. *
Ligands
PLP ×2
Waters ×334
* Residue conservation analysis
PDB id:
1kl7
Name: Lyase
Title: Crystal structure of threonine synthase from yeast
Structure: Threonine synthase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.70Å     R-factor:   0.201     R-free:   0.253
Authors: M.Garrido-Franco,S.Ehlert,A.Messerschmidt,S.Marinkovic,R.Hub B.Laber,G.P.Bourenkov,T.Clausen
Key ref:
M.Garrido-Franco et al. (2002). Structure and function of threonine synthase from yeast. J Biol Chem, 277, 12396-12405. PubMed id: 11756443 DOI: 10.1074/jbc.M108734200
Date:
11-Dec-01     Release date:   24-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16120  (THRC_YEAST) -  Threonine synthase
Seq:
Struc:
514 a.a.
509 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.3.1  - Threonine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Threonine Biosynthesis
      Reaction: O-phospho-L-homoserine + H2O = L-threonine + phosphate
O-phospho-L-homoserine
+ H(2)O
= L-threonine
+ phosphate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M108734200 J Biol Chem 277:12396-12405 (2002)
PubMed id: 11756443  
 
 
Structure and function of threonine synthase from yeast.
M.Garrido-Franco, S.Ehlert, A.Messerschmidt, S.Marinkovic', R.Huber, B.Laber, G.P.Bourenkov, T.Clausen.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Active site of yTS. a, schematic representation of the functionally important interactions within the active site. On the left side, hydrogen bonds between protein, water (dark balls) and cofactor (light gray) are indicated, whereas the fixation of the PLP pyridine ring is shown on the right side. b, detailed active site architecture. The internal aldimine is seen in light gray, water molecules are shown as dark balls, and the macrodipole of helix 10 is indicated. b was produced with DINO.
Figure 5.
Fig. 5. Mechanistic features of yTS. a, drawing of the modeled external aldimine between OPHS and PLP (light gray). Hydrogen bonds and interatomic distances (Å) relevant for substrate binding are indicated. b, mechanism of the reaction catalyzed by yTS where the substrate OPHS is converted to inorganic phosphate and threonine. The precise electron movements are indicated with arrows.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 12396-12405) copyright 2002.  
  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.  
19715325 G.K.Smith, Z.Ke, A.C.Hengge, D.Xu, D.Xie, and H.Guo (2009).
Active-site dynamics of SpvC virulence factor from Salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis.
  J Phys Chem B, 113, 15327-15333.  
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
18060821 Y.Zhu, H.Li, C.Long, L.Hu, H.Xu, L.Liu, S.Chen, D.C.Wang, and F.Shao (2007).
Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase.
  Mol Cell, 28, 899-913.
PDB codes: 2p1w 2q8y
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.