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Introduction

Every bacteria wants to live. Every bacteria wants to reproduce. To achieve both, bacteria need some sort of protection that will maintain the structure inside and will protect it from outside dangers. This protection is called cell wall, that primarily consists of a polymer that is called peptidoglycan. This compound can be synthesized only with the help of penicillin binding proteins (PBPs) , which are the target of this article (the name basically comes from a way it was discovered). PBP serves as a catalyst in the final stages of peptidoglycan synthesis, transglycosylation and transpeptidation in particular.^[2] Although there are multiple types of PBPs, they all bind penicillin (however, with different affinities) and this is what is important for this article.

As the bacteria infiltrates the organism, it becomes necessary to somehow destroy it. One way is to to break this cell wall. To achieve this, the penicillin is introduced to the bacteria that later reacts with PBPs (using β-lactam ring ), preventing it from catalyzing the formation of a peptidoglycan and, as a result, stops the formation of a cell wall. However, many pathogenic bacteria have evolved a way to mutate themselves to be immune to various drugs that contain this β-lactam rings. What happens is that bacterium produces enzyme, called β-lactamase that cleaves the β-lactam ring on a penicillin and thus preventing it from reacting with PBPs. To solve this problem, the new drug, called, lactivicin was developed that contains gamma-lactone rings and cycloserine as substitutions to β-lactam. So far, it has proved to be an efficient antibiotic. It successfully binds to PBPs and prevents cell wall from forming.

Recently, an analog of lactivicin, phenoxylactivicin (PLTV) was developed and is discussed in this article.

The complex of the PBP with phenoxylactivicin is shown on the picture.

Picture on the right is displayed as N-terminus to C-termiunus Rainbow for PBP complex . The coloring goes as shown on the sample:

Amino Terminus

Carboxy Terminus

Overall Structure

Penicillin Binding Proteins have specific structures and designs that promote allow the binding of Penicillin and other antibiotics. One of the enzymes within the PBP family is D-alanyl-D-alanine carboxypeptidase/transpeptidase. This enzyme is responsible for the link between two chains in the peptidoglycan network ^[3]. DA-DA peptidase’s structure contains a serine in the active site. Ser 62 is used to bind a peptide strand which would then link to another strand of the network, and this is the site where penicillin binds and inhibits the protein. This enzyme is split into two sections, which will be referred to as the North and South regions. The North Region contains both the carboxyl and amino termini, two α-helices, and a nine-stranded antiparallel β-sheet ^[4] This leads the Northern region of the enzyme to appear symmetrical. Both termini lead are connected to helices and then into β-strands. Inbetween the sets of strands the South region of the peptide is formed and this is strictly made out of helices. In the center of the two regions is where the Ser 62 active site resides, and this is also at the symmetrical center of the protein. The protein essentially forms a cupped hand, with the center of the palm being the active site, the bottom of the palm being a series of 8 or so helices, the knuckles being the β-strands, and the tips of the fingers being the two helices of the North region.

Binding Interactions

The final stages of the synthesis of peptidoglycan requires penicillin binding proteins. All bacterial cell walls are made of peptidoglycan and it is important to note that all bacteria have reactions that covalently link the first peptidoglycan between two polysaccharides. This reaction is catalyzed by transpeptidase enzymes which is inhibited by the beta-lactam. Penicillin binding protein binds to beta-lactam antibiotics because they are similar in chemical structure to the modular pieces that form the peptidoglycan. The beta-lactam amide bond is ruptured to form a covalent bond with the catalytic serine at the binding protein's active site. When the PBP form a stable covalent complex with the beta-lactam antibiotics, the cell dies due to PBP inactivation.

The beta-lactam area in most drugs resemble the D-Ala-D-Ala end of peptides to which the transpeptidase enzyme binds. At the DA-DA, there is a serine 62 which is used to bind peptide strands to other stands and this is also where penicillin binds and inhibits the protein. When the transpeptidase reaction takes place, the enzymes bind to the DA-DA end of the chain which results in one of the DA residues to be released and the enzyme attaches to the end of the peptide. Next, the closest peptidoglycan is covalently linked to the first peptidoglycan which forms a crosslink between the two polysaccharides. Almost every bacterium has PBP genes but most enzymes are inhibited by the beta-lactams. The enzymes become inactive due to the drugs binding tightly to the active site and blocking the reaction.

Additional Features

Antibiotics resistance is the property of bacteria that have receive relatively low effectiveness by antibiotic. With the overproduction and overusing of antibiotics, more bacteria have low resistance to antibiotic are killed than the bacteria have high resistance. Under the evolutionary pressure, the remaining group of bacteria have relatively high resistance which means that the normal antibiotics have less effectiveness or do not have effectiveness anymore. As penicillin-binding proteins playing an important role at bacteria’s cell synthesis and β-lactams antibiotics inhibiting bacterial division by binding penicillin-binding proteins, antibiotics resistance also emerges to the penicillin-binding proteins and makes penicillin-binding proteins have low affinity for penicillins.

Normally, the bacteria produce the penicillin binding proteins with low penicillin-affinity low affinity by transformation, which is a kind of gene modification. Through this way, bacteria could have a relatively higher resistance to β-lactams antibiotics. But staphylococcus is a special case, it strengthens the drug resistance by two ways instead of gene exchange. By the raised dissociation constants for the non-covalent pre-acylation and the dropped penicillin-sensitive microscopic rate constant for acylation, staphylococcus enhance its own drug resistance.^[5]

And the solution to the penicillin binding proteins drug resistance could be semi-synthetic β-lactams. The mechanism is that semi-synthetic β-lactams have the alternative side chain compared to the normal penicillins and it will make penicillin binding proteins have the higher affinity to it and as a result the increasing drug resistance will be solved.^[6]

Quiz Question 1

The binding pocket for PTLV (all residues within 5Å of the molecule) is shown here colored from most conserved to most variable.

Why are most of these residues highly conserved?

Would it be evolutionarily advantageous to mutate this binding pocket to prevent inhibition by PTLV? Explain.

See Also

• Penicillin-binding protein
• 2y2g
• 2bg1
• 2fff
• 2jch

Credits

Introduction - Anton El Khoury

Overall Structure - Tyler Carpenter

Drug Binding Site - Hyunjoon Choi

Additional Features - Tiankai Zhang

Quiz Question 1 - Samuel Pierce

References

1. ↑ Macheboeuf P, Fischer DS, Brown T Jr, Zervosen A, Luxen A, Joris B, Dessen A, Schofield CJ. Structural and mechanistic basis of penicillin-binding protein inhibition by lactivicins. Nat Chem Biol. 2007 Sep;3(9):565-9. Epub 2007 Aug 5. PMID:17676039 doi:10.1038/nchembio.2007.21
2. ↑ Pinho MG, Kjos M, Veening JW. How to get (a)round: mechanisms controlling growth and division of coccoid bacteria. Nat Rev Microbiol. 2013 Sep;11(9):601-14. doi: 10.1038/nrmicro3088. PMID:23949602 doi:http://dx.doi.org/10.1038/nrmicro3088
3. ↑ Goodsell, David. "Penicillin-binding Proteins." Penicillin-binding Proteins. May 2002. Web. 07 Apr. 2016.
4. ↑ Kelly, J. A., and A. P. Kuzin. "3PTE." RCSB PDB. Web. 07 Apr. 2016.
5. ↑ Fuda C, Suvorov M, Vakulenko SB, Mobashery S. The basis for resistance to beta-lactam antibiotics by penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus. J Biol Chem. 2004 Sep 24;279(39):40802-6. Epub 2004 Jun 28. PMID:15226303 doi:http://dx.doi.org/10.1074/jbc.M403589200
6. ↑ Ohi N, Aoki B, Shinozaki T, Moro K, Noto T, Nehashi T, Okazaki H, Matsunaga I. Semisynthetic beta-lactam antibiotics. I. Synthesis and antibacterial activity of new ureidopenicillin derivatives having catechol moieties. J Antibiot (Tokyo). 1986 Feb;39(2):230-41. PMID:3082839