PDBsum entry: 1yb0

Hydrolase

PDB-id: 1yb0

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

157 a.a. *

Ligands

PO4 ×3

Metal ions

_ZN ×3

Waters ×283

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1yb0

Name:

Hydrolase

Title:

Structure of plyl

Structure:

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

Source:

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

UniProt:

Chains A, B, C: Q81WA9 (Q81WA9_BACAN)

Seq:

234 a.a.

Struc:

157 a.a.

Key:

PfamA domain

Secondary structure

Enzyme class:

E.C.3.5.1.28   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.

Resolution:

1.86Å

R-factor:

0.206

R-free:

0.242

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:

18-Dec-04

Release date:

23-Aug-05

Quick_links

Procheck

Surface

Key reference

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.