Sandbox Reserved 1499
From Proteopedia
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<ref>DOI 10.1016/j.sbi.2010.09.014</ref> | <ref>DOI 10.1016/j.sbi.2010.09.014</ref> | ||
__TOC__ | __TOC__ | ||
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== Function == | == Function == | ||
| - | As a DD-carboxypeptidase, the function of PBP6 is to participate in the transpeptidation which occurs during the biosynthesis of peptidoglycan. 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. | + | As a DD-carboxypeptidase, the function of PBP6 is to participate in the transpeptidation which occurs during the biosynthesis of peptidoglycan. 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 | + | |
| - | Firstly, the PBP6 binds to carbonyl group in the peptide bond between the two terminal D-alanines of the N-acetylmuramic acid. This forms a high-energy tetrahedric intermediate called the acylenzyme. | + | The cleavage reaction takes place in two steps. |
| - | 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. | + | #Firstly, the PBP6 binds to carbonyl group in the peptide bond between the two terminal D-alanines of the N-acetylmuramic acid. 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. | ||
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== Structure== | == Structure== | ||
<StructureSection load='3ita' size='340' side='right' caption='PBP6, [[Resolution|resolution]] 1.80Å' scene='80/802673/Default/1'> | <StructureSection load='3ita' size='340' side='right' caption='PBP6, [[Resolution|resolution]] 1.80Å' scene='80/802673/Default/1'> | ||
| - | + | PBP6 is a monomeric enzyme with an N-terminal domain an C-terminal domain. | |
===Active site=== | ===Active site=== | ||
| - | The amino acids that compose the <scene name='80/802673/Active_site_1/1'>active site</scene> are: Ser40 and Lys43, which organised in a catalytic diad through a hydrogen bond, alongside with Ser106, | + | The amino acids that compose the <scene name='80/802673/Active_site_1/1'>active site</scene> 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. | 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. | ||
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When a substrate is fixated, the enzyme undergoes a conformation change (see below), which causes Lys43 to be exposed to the solvent. | 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. | 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. | ||
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===Binding site=== | ===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. | 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. | ||
Ser 83, specifically, is thought to be capable of stabilising the leaving group during the acylation reaction through hydrogen bonds. | Ser 83, 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. These nitrogens stabilise the carbonyl oxygen from the D-Ala-D-Ala peptide bond. | + | 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 stabilise the carbonyl oxygen from the D-Ala-D-Ala peptide bond. |
The Ser106, Thr210, Thr212 and Arg244 residues stabilise the C-terminal of the peptide through hydrogen bonds and bonds through water molecules (see structure [[3itb]]). | The Ser106, Thr210, Thr212 and Arg244 residues stabilise the C-terminal of the peptide through hydrogen bonds and bonds through water molecules (see structure [[3itb]]). | ||
| - | It can be seen that PBP6 presents both a binding site and an active site with a precise | + | It can be seen that PBP6 presents both a binding site and an active site with a precise configuration that makes it specific to its substrate. |
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===Ampicillin mimicry=== | ===Ampicillin mimicry=== | ||
| - | Ampicillin | + | Ampicillin stops the synthesis of peptidoglycan by competitive inhibition of PBP6. [[3ita]] shows the acylenzyme complex of PBP6 with ampicillin. |
| - | Ampicillin presents structural | + | Ampicillin presents structural characteristics which are similar to the enzyme substrate which allow it to bind to its active site. It however also possesses characteristics which allow it to stop the enzyme from functionning. It can use the same mechanisms as the enzyme substrate <scene name='80/802673/Active_site_amp/2'>to insert into the active site</scene>, and specifically the oxyanion hole. |
| + | Thanks to its O3 carboxylate group for example, it can insert It also forms a hydrogen bond with the Thr212 side chain. | ||
Similarly, Arg244 also binds to the C3 carboxylate group through a water molecule. | Similarly, Arg244 also binds to the C3 carboxylate group through a water molecule. | ||
| - | However, PBP6 cannot | + | 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 sterically hinders the interaction between Lys43 and the |
| - | <scene name='80/802673/Cat_water/2'>surrounding water molecules</scene>. As a result, no water molecule can be protonated in order to perform the | + | <scene name='80/802673/Cat_water/2'>surrounding water molecules</scene>. As a result, no water molecule can be protonated in order to perform the hydrolysis. |
It can be seen that through its structure, ampicilline imitates the natural substrate of PBP6 and stops it from performing its catalysis. | It can be seen that through its structure, ampicilline imitates the natural substrate of PBP6 and stops it from performing its catalysis. | ||
</StructureSection> | </StructureSection> | ||
== Relevance== | == Relevance== | ||
| - | The resolution of this structure played an important role in understanding the method of action of beta-lactam antibiotics<ref>DOI 10.1016/j.mib.2010.09.008</ref>. Due to the | + | The resolution of this structure played an important role in understanding the method of action of beta-lactam antibiotics<ref>DOI 10.1016/j.mib.2010.09.008</ref>. Due to the increase of antibiotic-resistant bacteria, it is important to understand the method of action of antibiotics in their every detail, so that treatments for resistent bacteria can be devised. |
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 22:01, 11 January 2019
| 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 functionning of the active site of PBP6 and of the role of pentapeptidic imitation by ampicillin. [2]
Contents |
Function
As a DD-carboxypeptidase, the function of PBP6 is to participate in the transpeptidation which occurs during the biosynthesis of peptidoglycan. 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 terminal D-alanines of the N-acetylmuramic acid. 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
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Relevance
The resolution of this structure played an important role in understanding the method of action of beta-lactam antibiotics[3]. Due to the increase of antibiotic-resistant bacteria, it is important to understand the method of action of antibiotics in their every detail, so that treatments for resistent 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
- ↑ 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
- ↑ 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
