6SSC

N-acetylmuramoyl-L-alanine amidase LysC from Clostridium intestinale URNW

Summary for 6SSC

• Entry DOI: 10.2210/pdb6ssc/pdb
• Related: 6SRT
• Descriptor: N-acetylmuramoyl-L-alanine amidase, PHOSPHATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: amidase, zinc binding, cell wall degradation, endolysine, hydrolase
• Biological source: Clostridium intestinale
• Total number of polymer chains: 1
• Total formula weight: 22731.93

Authors

Hakansson, M.,Al-Karadaghi, S.,Kovacic, R.,Plotka, M.,Kaczorowska, A.K.,Kaczorowski, T. (deposition date: 2019-09-06, release date: 2020-09-30, Last modification date: 2024-01-24)

Primary citation

Plotka, M.,Szadkowska, M.,Hakansson, M.,Kovacic, R.,Al-Karadaghi, S.,Walse, B.,Werbowy, O.,Kaczorowska, A.K.,Kaczorowski, T.
Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N -Terminal Extension.
Int J Mol Sci, 21:-, 2020

PubMed Abstract: Peptidoglycan hydrolytic enzymes are considered to be a promising alternative to conventional antibiotics in combating bacterial infections. To identify novel hydrolytic enzymes, we performed a database search with the sequences of two thermostable endolysins with high bactericidal activity, studied earlier in our laboratory. Both these enzymes originate from bacteriophages MAT2119 and vB_Tsc2631. A lytic enzyme LysC from URNW was found to have the highest amino acid sequence similarity to the bacteriophage proteins and was chosen for further analysis. The recombinant enzyme showed strong activity against its host bacteria , as well as against , , and , on average causing a 5.12 ± 0.14 log reduction of viable ATCC 25923 cells in a bactericidal assay. Crystallographic studies of the protein showed that the catalytic site of LysC contained a zinc atom coordinated by amino acid residues His, His, and Cys, a feature characteristic for type 2 amidases. Surprisingly, neither of these residues, nor any other of the four conserved residues in the vicinity of the active site, His, Thr, Tyr, and Thr, were essential to maintain the antibacterial activity of LysC. Therefore, our attention was attracted to the intrinsically disordered and highly positively charged -terminal region of the enzyme. Potential antibacterial activity of this part of the sequence, predicted by the Antimicrobial Sequence Scanning System, AMPA, was confirmed in our experimental studies; the truncated version of LysC (LysCΔ2-23) completely lacked antibacterial activity. Moreover, a synthetic peptide, which we termed Intestinalin, with a sequence identical to the first thirty amino acids of LysC, displayed substantial anti-staphylococcal activity with IC of 6 μg/mL (1.5 μM). This peptide was shown to have α-helical conformation in solution in the presence of detergents which is a common feature of amphipathic α-helical antimicrobial peptides.

PubMed: 32664473
DOI: 10.3390/ijms21144894

Experimental method

X-RAY DIFFRACTION (1.21 Å)