PDBsum entry 2d1f

Lyase

PDB id: 2d1f

Contents

Protein chains

349 a.a. *

Ligands

PLP ×2

Waters ×54

* Residue conservation analysis

PDB id:

2d1f

Name:

Lyase

Title:

Structure of mycobacterium tuberculosis threonine synthase

Structure:

Threonine synthase. Chain: a, b. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.191 R-free: 0.256

Authors:

A.S.Covarrubias,T.Bergfors,K.Mannerstedt,S.Oscarson,T.A.Jones, S.L.Mowbray,M.Hogbom

Key ref:

A.S.Covarrubias et al. (2008). Structural, biochemical, and in vivo investigations of the threonine synthase from Mycobacterium tuberculosis. J Mol Biol, 381, 622-633. PubMed id: 18621388 DOI: 10.1016/j.jmb.2008.05.086

Date:

20-Aug-05 Release date: 05-Sep-06

Protein chains

P9WG59  (THRC_MYCTU) -  Threonine synthase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 360 a.a.

Struc: 349 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.3.1 - threonine synthase.
• Pathway: Threonine Biosynthesis
• Reaction: O-phospho-L-homoserine + H2O = 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

reference

DOI no: 10.1016/j.jmb.2008.05.086

J Mol Biol 381:622-633 (2008)

PubMed id: 18621388

Structural, biochemical, and in vivo investigations of the threonine synthase from Mycobacterium tuberculosis.

A.S.Covarrubias, M.Högbom, T.Bergfors, P.Carroll, K.Mannerstedt, S.Oscarson, T.Parish, T.A.Jones, S.L.Mowbray.

ABSTRACT

Threonine biosynthesis is a general feature of prokaryotes, eukaryotic microorganisms, and higher plants. Since mammals lack the appropriate synthetic machinery, instead obtaining the amino acid through their diet, the pathway is a potential focus for the development of novel antibiotics, antifungal agents, and herbicides. Threonine synthase (TS), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the final step in the pathway, in which L-homoserine phosphate and water are converted into threonine and inorganic phosphate. In the present publication, we report structural and functional studies of Mycobacterium tuberculosis TS, the product of the rv1295 (thrC) gene. The structure gives new insights into the catalytic mechanism of TSs in general, specifically by suggesting the direct involvement of the phosphate moiety of the cofactor, rather than the inorganic phosphate product, in transferring a proton from C4' to C(gamma) in the formation of the alphabeta-unsaturated aldimine. It further provides a basis for understanding why this enzyme has a higher pH optimum than has been reported elsewhere for TSs and gives rise to the prediction that the equivalent enzyme from Thermus thermophilus will exhibit similar behavior. A deletion of the relevant gene generated a strain of M. tuberculosis that requires threonine for growth; such auxotrophic strains are frequently attenuated in vivo, indicating that TS is a potential drug target in this organism.

Selected figure(s)

Figure 3.
Fig. 3. Comparison of MtTS and TtTS active sites. Active-site residues of MtTS and the bound PLP are shown in gold, and equivalent residues of TtTS are in gray. Two important hydrogen bonds mentioned in the text are indicated by black dotted lines. Electron density is for the PLP in the last 2|F[o]| − |F[c]| map prior to its inclusion in the model, contoured at 1 σ = 0.2 e/Å^3.

Figure 5.
Fig. 5. Features of particular interest in the TS catalytic mechanism. A stereo view illustrates how the involvement of the PLP 5′-phosphate group in the conversion of β,γ-unsaturated ketimine to α,β-unsaturated aldimine is suggested by the proximity of the relevant groups in the modeled reaction intermediate, based on superposition of the Tt–AP5 structure (shown by dotted lines). Residues that could influence the pH optimum, as discussed in the text, are shown for MtTS (gold carbons) and EcTS (cyan carbons).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 622-633) copyright 2008.

Figures were selected by an automated process.