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This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

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Penicillin-binding protein 6 from Escherichia coli

The Penicillin-binding protein 6 (PBP6) from Escherichia coli is a DD-carboxypeptidase which plays an important role in the creation of the bacterial cell wall. It belongs to the group of PBP of low molecular mass. Its structure was determined by Chen et al.^[1]. These results allow for the study of the functioning of the active site of PBP6 and of the role of pentapeptidic imitation by ampicillin.

1 Penicillin-binding protein 6 from Escherichia coli
2 Function
3 Structure
4 Relevance
5 References

Function

As a DD-carboxypeptidase, the function of PBP6 is to participate in the transpeptidation which occurs during the biosynthesis of peptidoglycan ^[2]. More specifically, it cleaves the peptide bond between the two terminal D-alanines of the pentapeptidic muramyl peptides of sequence L-Ala-D-Glu-m-A2pm-D-Ala-D-Ala. This then allows transpeptidases to create peptidoglycan cross-links which stabilise the cell wall.

The cleavage reaction takes place in two steps.

Firstly, the PBP6 binds to carbonyl group in the peptide bond between the two C-terminal D-alanines of the N-acetylmuramic acid^[3]. This forms a high-energy tetrahedric intermediate called the acylenzyme.
The acylenzyme allows the medium to reach the carbonyle group. As a result, a water molecule can attack the group, causing the cleavage of the tetrahedral structure.

Structure

PBP6 is a monomeric enzyme with a C-terminal domain rich in beta-sheets and an active site localised near its N-terminal domain^[4].

Active site

The amino acids that compose the are: Ser40 and Lys43, which are organised in a catalytic diad through a hydrogen bond, alongside with Ser106, Asp108, Lys209 and Thr210.

The oxygen from Ser40 binds to the carbon from the peptide bond between the two D-alanines, which causes the formation of the acylenzyme complex after the terminal D-alanine leaves.

When a substrate is fixated, the enzyme undergoes a conformation change (see below), which causes Lys43 to be exposed to the solvent.

Lys43 deprotonates a catalytic water molecule which then binds to the carbon from the acylenzyme complex in order to regenerate the enzyme and free the peptide which has been shortened by one amino acid.

Binding site

Other amino acids allow the selective fixation of the ligand to the enzyme. The residues 79 to 83, 212 to 218 and 242 to 248 are responsible for this. These residues undergo a conformation change during substrate fixation which changes the configuration of the entire enzyme and gives the substrate access to the active site.

Ser83, specifically, is thought to be capable of stabilising the leaving group during the acylation reaction through hydrogen bonds.

Another important part of the selective fixation process is the oxyanion hole, which is a hole in the enzyme structure created by the backbone nitrogens of Ser40 and Thr212. These nitrogens can interact with the carbonyl oxygen from the D-Ala-D-Ala peptide bond, thus stabilising it.

The Ser106, Thr210, Thr212 and Arg244 residues stabilise the C-terminal of the substrate thanks to hydrogen bonding and bonds through water molecules (see structure 3itb).

These features show that PBP6 presents both a binding site and an active site with a precise configuration that makes it highly specific to its substrate.

Ampicillin mimicry

Ampicillin stops the synthesis of peptidoglycan by competitive inhibition of PBP6. 3ita shows the acylenzyme complex of PBP6 with ampicillin.

Ampicillin presents structural characteristics which are similar to the PBP6's substrate. These characteristics allow it to bind to the enzyme and access its active site. It however also possesses characteristics which allow it to stop the enzyme from functioning.

It uses the same mechanisms as the enzyme substrate . Thanks to its O3 carboxylate group for example, it can mimic the carbonyl oxygen from the peptide bond and make use of the oxyanion hole described previously. The oxygen atom in question additionally forms a hydrogen bond with the Thr212 side chain.

Similarly, the C3 carboxylate group can bind to Arg244 through a water molecule, as the substrate would.

However, PBP6 cannot hydrolyse the amide bond from ampicillin. This is due to the bond in question being contained inside the beta-lactam cycle of the antibiotic. Additionally, the sulfur atom from the ampicillin molecule hinders the interaction between Lys43 and the

. As a result, no water molecule can be protonated in order to perform the hydrolysis.

Through its pentapeptidic-imitating structure, ampicilline mimics the natural substrate of PBP6 and stops it from performing its catalysis.

Relevance

The resolution of this structure plays an important role in understanding the exact method of action of beta-lactam antibiotics^[5]. Since antibiotic resistance is often based on small changes in protein conformation at the molecular level, it is important to understand the method of action of antibiotics in their every detail, so that treatments for resistant bacteria can be devised.

References

↑ Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 2009 Oct 14;131(40):14345-54. PMID:19807181 doi:10.1021/ja903773f
↑ Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008 Mar;32(2):234-58. doi: 10.1111/j.1574-6976.2008.00105.x., Epub 2008 Feb 11. PMID:18266856 doi:http://dx.doi.org/10.1111/j.1574-6976.2008.00105.x
↑ Mattei PJ, Neves D, Dessen A. Bridging cell wall biosynthesis and bacterial morphogenesis. Curr Opin Struct Biol. 2010 Dec;20(6):749-55. doi: 10.1016/j.sbi.2010.09.014., Epub 2010 Oct 26. PMID:21030247 doi:http://dx.doi.org/10.1016/j.sbi.2010.09.014
↑ van Heijenoort J. Peptidoglycan hydrolases of Escherichia coli. Microbiol Mol Biol Rev. 2011 Dec;75(4):636-63. doi: 10.1128/MMBR.00022-11. PMID:22126997 doi:http://dx.doi.org/10.1128/MMBR.00022-11
↑ Llarrull LI, Testero SA, Fisher JF, Mobashery S. The future of the beta-lactams. Curr Opin Microbiol. 2010 Oct;13(5):551-7. doi: 10.1016/j.mib.2010.09.008. Epub, 2010 Sep 29. PMID:20888287 doi:http://dx.doi.org/10.1016/j.mib.2010.09.008

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Sandbox Reserved 1499

From Proteopedia

Penicillin-binding protein 6 from Escherichia coli

Contents

Function

Structure

Active site

Binding site

Ampicillin mimicry

Relevance

References

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