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See detailStructure of PBP-A from Thermosynechococcus elongatus, a Penicillin-Binding Protein Closely Related to Class A β-Lactamases
Urbach, Carole; Evrard, Christine ULg; Pudzaitis, Vaidas et al

in Journal of Molecular Biology (2009), 386

Molecular evolution has always been a subject of discussions, and researchers are interested in understanding how proteins with similar scaffolds can catalyze different reactions. In the superfamily of ... [more ▼]

Molecular evolution has always been a subject of discussions, and researchers are interested in understanding how proteins with similar scaffolds can catalyze different reactions. In the superfamily of serine penicillin-recognizing enzymes, D-alanyl-D-alanine peptidases and β-lactamases are phylogenetically linked but feature large differences of reactivity towards their respective substrates. In particular, while β-lactamases hydrolyze penicillins very fast, leading to their inactivation, these molecules inhibit D-alanyl-D-alanine peptidases by forming stable covalent penicilloyl enzymes. In cyanobacteria, we have discovered a new family of penicillin-binding proteins (PBPs) presenting all the sequence features of class A β-lactamases but having a six-amino-acid deletion in the conserved Ω-loop and lacking the essential Glu166 known to be involved in the penicillin hydrolysis mechanism. With the aim of evolving a member of this family into a β-lactamase, PBP-A from Thermosynechococcus elongatus has been chosen because of its thermostability. Based on sequence alignments, introduction of a glutamate in position 158 of the shorter Ω-loop afforded an enzyme with a 50-fold increase in the rate of penicillin hydrolysis. The crystal structures of PBP-A in the free and penicilloylated forms at 1.9 Å resolution and of L158E mutant at 1.5 Å resolution were also solved, giving insights in the catalytic mechanism of the proteins. Since all the active-site elements of PBP-A-L158E, including an essential water molecule, are almost perfectly superimposed with those of a class A β-lactamase such as TEM-1, the question why our mutant is still 5 orders of magnitude less active as a penicillinase remains and our results emphasize how far we are from understanding the secrets of enzymes. Based on the few minor differences between the active sites of PBP-A and TEM-1,mutations were introduced in the L158E enzyme, but while activities on D-Ala-D-Ala mimicking substrates were severely impaired, further improvement in penicillinase activity was unsuccessful. [less ▲]

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See detailThe incorporation of a non-natural amino acid (aza-tryptophan) may help to crystallize a protein and to solve its crystal structure. Application to bacteriophage lambda lysozyme.
Evrard, Christine ULg; Fastrez, Jacques; Declercq, Jean-Paul

in Acta Crystallographica Section D-Biological Crystallography (1999), D55

Until now, wild-type bacteriophage lambda lysozyme had been impossible to crystallize. This difficulty could be overcome by the replacement of the four tryptophan residues by azatryptophans. Analysis of ... [more ▼]

Until now, wild-type bacteriophage lambda lysozyme had been impossible to crystallize. This difficulty could be overcome by the replacement of the four tryptophan residues by azatryptophans. Analysis of the intermolecular and intramolecular contacts in this modification allows understanding of the differences in behaviour between the native and modified molecules. Furthermore, this mutation was very useful for the creation of new heavy-atom binding sites and for the solution of the non-crystallographic symmetry, which is extremely important for phase improvement. This procedure seems to be generally applicable, at least in the search for new possibilities for heavy-atom binding sites. [less ▲]

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See detailHistidine modification and mutagenesis point to the involvement of a large conformational change in the mechanism of action of phage lambda lysozyme
Evrard, Christine ULg; Fastrez, Jacques; Soumillion, Patrice

in FEBS Letters (1999), 460

Phage lambda lysozyme is structurally related to other known lysozymes but its mechanism of action is different from the classical lysozyme mechanism, acting as a transglycosidase rather than a hydrolase ... [more ▼]

Phage lambda lysozyme is structurally related to other known lysozymes but its mechanism of action is different from the classical lysozyme mechanism, acting as a transglycosidase rather than a hydrolase. As two conformations have been revealed by the crystal structure, we investigated the effect of mutating and modifying a histidine located near to or far from the active site in the respective closed and open conformations. Whereas its asparagine mutation has little or no effect on activity, its N-carbethoxylation inactivates the enzyme. This provide further evidence for the involvement of the closed conformation and for the need of conformational mobility in lambda lysozyme function. [less ▲]

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See detailCrystal Structure of the Lysozyme from Bacteriophage Lambda and its Relationship with V and C-type Lysozymes
Evrard, Christine ULg; Fastrez, Jacques; Declercq, Jean-Paul

in Journal of Molecular Biology (1998), 276

Like other lysozymes, the bacteriophage lambda lysozyme is involved in the digestion of bacterial walls. This enzyme is remarkable in that its mechanism of action is different from the classical lysozyme ... [more ▼]

Like other lysozymes, the bacteriophage lambda lysozyme is involved in the digestion of bacterial walls. This enzyme is remarkable in that its mechanism of action is different from the classical lysozyme's mechanism. From the point of view of protein evolution, it shows features of lysozymes from different classes. The crystal structure of the enzyme in which all tryptophan residues have been replaced by aza-tryptophan has been solved by X-ray crystallography at 2.3 Å using a combination of multiple isomorphous replacement, non-crystallographic symmetry averaging and density modification techniques. There are three molecules in the asymmetric unit. The characteristic structural elements of lysozymes are conserved: each molecule is organized in two domains connected by a helix and the essential catalytic residue (Glu19) is located in the depth of a cleft between the two domains. This cleft shows an open conformation in two of the independent molecules, while access to the cavity is much more restricted in the last one. A structural alignment with T4 lysozyme and hen egg white lysozyme allows us to superpose about 60 Cα atoms with a rms distance close to 2 Å. The best alignments concern the helix preceding the catalytic residue, some parts of the beta sheets and the helix joining the two domains. The results of sequence alignments with the V and C lysozymes, in which weak local similarities had been detected, are compared with the structural results. [less ▲]

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See detailCrystallization and preliminary X-ray analysis of bacteriophage lambda lysozyme in which all tryptophans have been replaced by aza-tryptophans
Evrard, Christine ULg; Declercq, Jean-Paul; Fastrez, Jacques

in Acta Crystallographica Section D-Biological Crystallography (1997), D53

After many unsuccessful attempts to crystallize the bacteriophage lambda lysozyme, a mutant where all the tryptophan residues have been replaced by aza-tryptophans has been crystallized by the vapor ... [more ▼]

After many unsuccessful attempts to crystallize the bacteriophage lambda lysozyme, a mutant where all the tryptophan residues have been replaced by aza-tryptophans has been crystallized by the vapor-diffusion method. The crystals are orthorhombic and belong to space group P212121 with cell dimensions a = 73.01, b = 78.80, c = 82.31 Å. Diffraction data were collected using synchrotron radiation sources. Crystals diffract to a resolution of 2.3 Å. Data from two different platinum derivatives were also recorded to 2.8 and 2.5 Å, respectively. [less ▲]

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