PDBsum entry 3rdr

Hydrolase

PDB id: 3rdr

Contents

Protein chain

153 a.a.

Metals

_CL

_ZN

Waters ×65

PDB id:

3rdr

Name:

Hydrolase

Title:

Structure of the catalytic domain of xlya

Structure:

N-acetylmuramoyl-l-alanine amidase xlya. Chain: a. Synonym: autolysin, cell wall hydrolase. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: xlya, bsu12810. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.219 R-free: 0.235

Authors:

L.Y.Low,R.C.Liddington

Key ref:

L.Y.Low et al. (2011). Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins. J Biol Chem, 286, 34391-34403. PubMed id: 21816821 DOI: 10.1074/jbc.M111.244160

Date:

01-Apr-11 Release date: 10-Aug-11

Supersedes:

3hma

Protein chain

P39800  (XLYA_BACSU) -  N-acetylmuramoyl-L-alanine amidase XlyA from Bacillus subtilis (strain 168)

Seq: 297 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.28 - N-acetylmuramoyl-L-alanine amidase.
• Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.

DOI no: 10.1074/jbc.M111.244160

J Biol Chem 286:34391-34403 (2011)

PubMed id: 21816821

Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins.

L.Y.Low, C.Yang, M.Perego, A.Osterman, R.Liddington.

ABSTRACT

The recombinant lysins of lytic phages, when applied externally to Gram-positive bacteria, can be efficient bactericidal agents, typically retaining high specificity. Their development as novel antibacterial agents offers many potential advantages over conventional antibiotics. Protein engineering could exploit this potential further by generating novel lysins fit for distinct target populations and environments. However, access to the peptidoglycan layer is controlled by a variety of secondary cell wall polymers, chemical modifications, and (in some cases) S-layers and capsules. Classical lysins require a cell wall-binding domain (CBD) that targets the catalytic domain to the peptidoglycan layer via binding to a secondary cell wall polymer component. The cell walls of Gram-positive bacteria generally have a negative charge, and we noticed a correlation between (positive) charge on the catalytic domain and bacteriolytic activity in the absence of the CBD (nonclassical behavior). We investigated a physical basis for this correlation by comparing the structures and activities of pairs of lysins where the lytic activity of one of each pair was CBD-independent. We found that by engineering a reversal of sign of the net charge of the catalytic domain, we could either eliminate or create CBD dependence. We also provide evidence that the S-layer of Bacillus anthracis acts as a molecular sieve that is chiefly size-dependent, favoring catalytic domains over full-length lysins. Our work suggests a number of facile approaches for fine-tuning lysin activity, either to enhance or reduce specificity/host range and/or bactericidal potential, as required.