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PDB:1ZAT

Protein Name

Peptideglycan L,D-transpeptidase

Species

Enterococcus faecium

Biological Context

β-lactam is one of the most widely antibiotics used for the treatment of bacterial infections. β-lactams are toxic to bacteria since they inhibit the enzymes that are essential for cell wall synthesis. However, some bacteria show β-lactam-resistance due to the production of β-lactam-insensitive enzymes for cell wall synthesis or β lactam-degrading enzymes. The protein described here, E. faecium peptideglycan L,D-transpeptidase(Ldt), is a β-lactam-insensitive enzymes for peptide transfer reaction during cell wall synthesis. In E. faecium, the peptide transfer reaction is mainly catalyzed by D,D-transpeptidase which is sensitive to β-lactams. In mutant E. faecium which expresses Ldt , on the other hand, the reaction proceeds despite in the presence of β-lactams. The peptide transfer reactions by Ldt and Ddt are shown in fig1.

fig1

fig1. Peptide transfer reactions of Ldt(upper) and Ddt(lower). Ldt forms a peptide bond between L-Lys and D-iGln, while Ddt forms a peptide bond between D-Ala and D-iGln.

Structure Description

1zat1zat_x1zat_y

Shown is the active fragment (217-466) of the whole Ltd, which is divided to N terminal (residue 217- 338) and C terminal domain (residue 339-466). The N terminal domain contains mixed α-β fold, containing four α-helices and nine β-strands (fig2 red). This domain would function as a pedestal, placing the C terminal domain in the proximity of substrate. On the other hand, the C terminal domain folds into globular structure mainly composed of two parallel β sheet(fig2 blue). This domain belongs to “ErfK_YbiS_YhnG domain”, which is conserved module of 357 eubacterial proteins. Although the function of many proteins of this family is not well-characterized, that of Ldt is known as the active site of the peptide transfer reaction. Cys442 in the C terminal domain of Ldt is the critical residue for the reaction. This cystein residue is localized in a buried pocket and is accessible by two paths on different sides of the C terminal domain (fig3). These two paths to the catalytic residue are supposed to be the binding sites for the acceptor and donor substrates of the peptide transfer reaction.

fig2

fig2. Overall structure of Ldt. N terminal- and C terminal domains are colored red and green, respectively.

fig3a ~ fig3b

fig3. Two paths to the active center in C terminal domain. N terminal domain, C terminal domain, and the active center residue (Cys442) are colored red, green, and yellow.

Protein Data Bank (PDB)

References

Source

Biarrotte-Sorin, S. Hugonnet, J.E. Delfosse, V. Mainardi, J.L. Gutmann, L. Arthur, M. Mayer, C.; "Crystal Structure of a Novel beta-Lactam-insensitive Peptidoglycan Transpeptidase."; J.Mol.Biol.; (2006) 359:533-538 PubMed:16647082.

Others

author: Daisuke Ino


Japanese version:PDB:1ZAT