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

Experimental Data Snapshot

  • Resolution: 1.21 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

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Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N -Terminal Extension.

Plotka, M.Szadkowska, M.Hakansson, M.Kovacic, R.Al-Karadaghi, S.Walse, B.Werbowy, O.Kaczorowska, A.K.Kaczorowski, T.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21144894
  • Primary Citation of Related Structures:  
    6SSC, 6SU5

  • 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 Thermus scotoductus bacteriophages MAT2119 and vB_Tsc2631. A lytic enzyme LysC from Clostridium intestinale 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 C. intestinale , as well as against C. sporogenes , Bacillus cereus , Micrococcus luteus, and Staphylococcus aureus , on average causing a 5.12 ± 0.14 log reduction of viable S. aureus 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 50 , His 147 , and Cys 155 , 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 51 , Thr 52 , Tyr 76 , and Thr 153 , were essential to maintain the antibacterial activity of LysC. Therefore, our attention was attracted to the intrinsically disordered and highly positively charged N -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 50 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.

  • Organizational Affiliation

    Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylmuramoyl-L-alanine amidase192Clostridium intestinaleMutation(s): 0 
Gene Names: CINTURNW_1763
Find proteins for U2NM08 (Clostridium intestinale URNW)
Explore U2NM08 
Go to UniProtKB:  U2NM08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2NM08
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.21 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.4α = 90
b = 53.78β = 90
c = 76.71γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilSweden685778

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description