PDBsum entry 3hmb

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
154 a.a. *
_ZN ×3
Waters ×149
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Mutant endolysin from bacillus subtilis
Structure: N-acetylmuramoyl-l-alanine amidase xlya. Chain: a, b, c. Synonym: cell wall hydrolase, autolysin. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: xlya, bsu12810. Expressed in: escherichia coli. Expression_system_taxid: 562
2.70Å     R-factor:   0.213     R-free:   0.249
Authors: L.Y.Low,R.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
29-May-09     Release date:   09-Jun-10    
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Protein chains
Pfam   ArchSchema ?
P39800  (XLYA_BACSU) -  N-acetylmuramoyl-L-alanine amidase XlyA
297 a.a.
154 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - N-acetylmuramoyl-L-alanine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptidoglycan catabolic process   1 term 
  Biochemical function     N-acetylmuramoyl-L-alanine amidase activity     1 term  


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.
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.