Crystal Structures of Active LytM

Firczuk, Małgorzata; Mucha, Artur; Bochtler, Matthias

doi:10.1016/j.jmb.2005.09.082

Cited by 100 publications

(144 citation statements)

References 29 publications

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“…The N-terminal domain of gp13⌬C had a structure closely similar to hen egg white lysozyme (Dali Z-score of 6.4) (22) and the C-terminal domain was similar to the active form of LytM (23) [Protein Data Bank (PDB) ID code 2B0P] a metalloendopeptidase (Z score of 11.3) in the M23 family (24). The linker polypeptide between the two domains consists of six sequential glycine residues (160-165) defined by rather poor electron density in the gp13⌬C map, indicative of flexibility (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage φ29 tail

Xiang

Morais

Cohen

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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The small bacteriophage 29 must penetrate the Ϸ250-Å thick external peptidoglycan cell wall and cell membrane of the Grampositive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage 29 is noncontractile and Ϸ380 Å long. A 1.8-Å resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N-and C-terminal domains, whose structures resemble lysozyme-like enzymes and metalloendopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the 29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13 ؊ mutants with the 29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.hydrolase ͉ infection ͉ structure ͉ zinc ion

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Section: Resultsmentioning

confidence: 99%

“…The zinc ion is not solvent accessible in inactive LytM (23,32). A proteolytic modification is required for activation of the enzyme that cleaves a loop blocking the active center.…”

Section: Resultsmentioning

confidence: 99%

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage φ29 tail

Xiang

Morais

Cohen

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…Crystal structures have been determined for inactive [16] and active [17] forms of the zoocin/ lysostaphin homolog LytM. The inactive form has side chain nitrogens of H210 and H293, and side chain oxygens of N117 and D214 as ligands, while the active form has H210, H293, D214, and water or a buffer anion as ligands.…”

Section: Resultsmentioning

confidence: 99%

“…Active LytM was crystallized in different forms and a confusing substitution of the fourth Oligand was observed [17]. Depending upon crystallization buffer, phosphate, cacodylate, or tartrate was found, while the expectation was that water would be the physiologically relevant ligand in analogy to other zinc metallopeptidases.…”

Section: Resultsmentioning

confidence: 99%

“…Discussion of specific amino acid residues in zoocin and any of its recombinant forms will use the sequence numbering of NCIB entry gi/2804351, while residues for lysostaphin will use NCIB entry gi/2072411. Discussion of the homolog LytM will use the numbering scheme adopted in the publication of its crystal structures [16,17], which are 25 higher than the sequence in NCIB entry gi/42543452 which is missing a 25 residue leader sequence.…”

Section: Methodsmentioning

confidence: 99%

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The metal binding site of zoocin A

et al. 2008

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Direct metal analysis of the bacteriolytic exoenzyme zoocin A failed to unequivocally identify a putative metal cofactor. Hence, indirect experiments utilizing NMR were undertaken to settle this question. Cd +2 as a surrogate metal ion was reconstituted into EDTA-treated, metal-free recombinant zoocin, and 113 Cd-NMR was employed to explore binding in the protein for this ion. The Cdsubstituted enzyme was found to have 75% of native streptococcolytic activity. A major 113 Cd resonance at 113.6 ppm was observed which with time split into resonances at 113.6 and 107.2 ppm. A minor 113 Cd resonance at 87.3 ppm was observed which increased in intensity with time. These Cd chemical shifts are indicative of two nitrogen atoms and two oxygen atoms ligating directly to the metal site. Based upon conserved amino acid residues in a homologous protein of known structure, LytM, the ligands in zoocin are tentatively assigned to H45, D49, H133, and some combination of water or buffer ions as the fourth oxygen donor in zoocin A. Comparison of the combined intensities for 113 Cd-substituted zoocin with a known quantity of another Cd-substituted protein gave Cdbinding as approximately stoichiometric (1.2 +/-0.2) with protein. Additional metal-removal and reconstitution experiments on the recombinant catalytic domain of zoocin implicate Zn +2 as the metal cofactor. Therefore, the evidence supports zoocin as a single Zn ion binding metalloenzyme.

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Synthesis and Antibacterial Activity Evaluation of Imidazole Derivatives Containing 6‐Methylpyridine Moiety

Yuan

Sun

et al. 2023

Chemistry & Biodiversity

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A series of 2‐cyclopropyl‐5‐(5‐(6‐methylpyridin‐2‐yl)‐2‐substituted‐1H‐imidazol‐4‐yl)‐6‐phenylimidazo[2,1‐b][1,3,4]thiadiazoles (15a–t and 16a–f) were synthesized and their antibacterial activities were evaluated. More than half of the compounds showed moderate or strong antibacterial activity. Among them, compounds 15t (MIC=1–2 μg/mL) and 16d (MIC=0.5 μg/mL) showed the strongest antibacterial activities. Notably, compound 16d did not exhibit cytotoxicity in HepG2 cells and did not show hemolysis like the positive control compound Gatifloxacin. The results suggest that compound 16d should be further investigated as a candidate antibacterial agent.

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Crystal Structures of Active LytM

Cited by 100 publications

References 29 publications

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage φ29 tail

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage φ29 tail

The metal binding site of zoocin A

Synthesis and Antibacterial Activity Evaluation of Imidazole Derivatives Containing 6‐Methylpyridine Moiety

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