PDBsum entry: 2ar3

Hydrolase

PDB id: 2ar3

Contents

Protein chains

157 a.a. *

Ligands

PO4 ×3

Metals

_ZN ×3

Waters ×149

* Residue conservation analysis

PDB id:

2ar3

Name:

Hydrolase

Title:

E90a mutant structure of plyl

Structure:

Prophage lambdaba02, n-acetylmuramoyl-l-alanine amidase, family 2. Chain: a, b, c. Fragment: catalytic domain. Engineered: yes. Mutation: yes

Source:

Bacillus anthracis. Organism_taxid: 1392. Gene: sterne. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.226 R-free: 0.256

Authors:

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

Key ref:

L.Y.Low et al. (2005). Structure and lytic activity of a Bacillus anthracis prophage endolysin. J Biol Chem, 280, 35433-35439. PubMed id: 16103125 DOI: 10.1074/jbc.M502723200

Date:

19-Aug-05 Release date: 06-Jun-06

Protein chains

Q81WA9  (Q81WA9_BACAN) -  Prophage LambdaBa02, N-acetylmuramoyl-L-alanine amidase PlyL

Seq: 234 a.a.

Struc: 157 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.

 Gene Ontology (GO) functional annotation 

• Biological process: peptidoglycan catabolic process (1 term)
• Biochemical function: N-acetylmuramoyl-L-alanine amidase activity (1 term)

DOI no: 10.1074/jbc.M502723200

J Biol Chem 280:35433-35439 (2005)

PubMed id: 16103125

Structure and lytic activity of a Bacillus anthracis prophage endolysin.

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

ABSTRACT

We report a structural and functional analysis of the lambda prophage Ba02 endolysin (PlyL) encoded by the Bacillus anthracis genome. We show that PlyL comprises two autonomously folded domains, an N-terminal catalytic domain and a C-terminal cell wall-binding domain. We determined the crystal structure of the catalytic domain; its three-dimensional fold is related to that of the cell wall amidase, T7 lysozyme, and contains a conserved zinc coordination site and other components of the catalytic machinery. We demonstrate that PlyL is an N-acetylmuramoyl-L-alanine amidase that cleaves the cell wall of several Bacillus species when applied exogenously. We show, unexpectedly, that the catalytic domain of PlyL cleaves more efficiently than the full-length protein, except in the case of Bacillus cereus, and using GFP-tagged cell wall-binding domain, we detected strong binding of the cell wall-binding domain to B. cereus but not to other species tested. We further show that a related endolysin (Ply21) from the B. cereus phage, TP21, shows a similar pattern of behavior. To explain these data, and the species specificity of PlyL, we propose that the C-terminal domain inhibits the activity of the catalytic domain through intramolecular interactions that are relieved upon binding of the C-terminal domain to the cell wall. Furthermore, our data show that (when applied exogenously) targeting of the enzyme to the cell wall is not a prerequisite of its lytic activity, which is inherently high. These results may have broad implications for the design of endolysins as therapeutic agents.

Selected figure(s)

Figure 3.
FIGURE 3. Stereo views of PlyL and active site comparisons. A, stereo C representation of PlyL. Amino acids differences between PlyL and PlyG are indicated. Most of these are surface-exposed except for Val-55, which makes hydrophobic contacts with Trp-68 in PlyL. In PlyG, the Val-55 is replaced by the larger residue Ile, but this is complemented by a change to the smaller Leu in place of Trp-68. B, stereo view of the active site residues of PlyL (light gray), T7 lysozyme (PDB: 1LBA [PDB] ) (medium gray), and PGRP-LB (PDB: 1OHT [PDB] ) (dark gray).

Figure 5.
FIGURE 5. A proposed model of species-specific activation of PlyL. A, in full-length PlyL, the C-terminal domain (gray oval) binds to and suppresses the catalytic activity of the N-terminal domain (blue square) allosterically. B, binding of the C-terminal domain to a cell-wall component (shown by black cross) characteristic of a cognate bacterium (such as B. cereus) releases the constraints on the catalytic domain, allowing it to adopt an alternative, active, conformation. In the absence of such an interaction partner, as in the case of B. subtilis, B. megaterium or a free peptidoglycan in vitro, the full-length PlyL would exist mostly in the inactive conformation. C, a truncation of the C-terminal domain maintains the enzyme in a constitutively active form.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 35433-35439) copyright 2005.

Figures were selected by an automated process.