6AKV

Crystal structure of LysB4, the endolysin from Bacillus cereus-targeting bacteriophage B4

Summary for 6AKV

• Entry DOI: 10.2210/pdb6akv/pdb
• Descriptor: LysB4, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: endolysin, las type enzyme, l-alanoyl d-glutamate endopeptidase, hydrolase
• Biological source: Bacillus phage B4
• Total number of polymer chains: 1
• Total formula weight: 30280.20

Authors

Hong, S.,Ha, N.-C. (deposition date: 2018-09-03, release date: 2019-02-13, Last modification date: 2023-11-22)

Primary citation

Hong, S.,Son, B.,Ryu, S.,Ha, N.C.
Crystal Structure of LysB4, an Endolysin fromBacillus cereus-Targeting Bacteriophage B4.
Mol. Cells, 42:79-86, 2019

PubMed Abstract: Endolysins are bacteriophage-derived enzymes that hydrolyze the peptidoglycan of host bacteria. Endolysins are considered to be promising tools for the control of pathogenic bacteria. LysB4 is an endolysin produced by -infecting bacteriophage B4, and consists of an N-terminal enzymatic active domain (EAD) and a C-terminal cell wall binding domain (CBD). LysB4 was discovered for the first time as an Lalanoyl-D-glutamate endopeptidase with the ability to breakdown the peptidoglycan among -infecting phages. To understand the activity of LysB4 at the molecular level, this study determined the X-ray crystal structure of the LysB4 EAD, using the full-length LysB4 endolysin. The LysB4 EAD has an active site that is typical of LAS-type enzymes, where Zn is tetrahedrally coordinated by three amino acid residues and one water molecule. Mutational studies identified essential residues that are involved in lytic activity. Based on the structural and biochemical information about LysB4, we suggest a ligand-docking model and a putative endopeptidase mechanism for the LysB4 EAD. These suggestions add insight into the molecular mechanism of the endolysin LysB4 in -infecting phages.

PubMed: 30518175
DOI: 10.14348/molcells.2018.0379

Experimental method

X-RAY DIFFRACTION (2.4 Å)