PDBsum entry: 2ixu

Hydrolase

PDB id: 2ixu

Contents

Protein chain

338 a.a. *

Ligands

NAG-MU2

FMT

Waters ×172

* Residue conservation analysis

PDB id:

2ixu

Name:

Hydrolase

Title:

Crystal structure of the modular cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin)

Structure:

Lysozyme. Chain: a. Synonym: endolysin, muramidase, cp-1 lysin, cpl-1. Engineered: yes

Source:

Streptococcus phage cp-1. Cp-1 bacteriophage. Organism_taxid: 10747. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: dh1

Resolution:

2.28Å R-factor: 0.212 R-free: 0.262

Authors:

I.Perez-Dorado,J.A.Hermoso

Key ref:

I.Pérez-Dorado et al. (2007). Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1. J Biol Chem, 282, 24990-24999. PubMed id: 17581815 DOI: 10.1074/jbc.M704317200

Date:

11-Jul-06 Release date: 03-Jul-07

Protein chain

P15057  (LYS_BPCP1) -  Lysozyme

Seq: 339 a.a.

Struc: 338 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - Lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (6 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1074/jbc.M704317200

J Biol Chem 282:24990-24999 (2007)

PubMed id: 17581815

Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1.

I.Pérez-Dorado, N.E.Campillo, B.Monterroso, D.Hesek, M.Lee, J.A.Páez, P.García, M.Martínez-Ripoll, J.L.García, S.Mobashery, M.Menéndez, J.A.Hermoso.

ABSTRACT

Pneumococcal bacteriophage-encoded lysins are modular proteins that have been shown to act as enzymatic antimicrobial agents (enzybiotics) in treatment of streptococcal infections. The first x-ray crystal structures of the Cpl-1 lysin, encoded by the pneumococcal phage Cp-1, in complex with three bacterial cell wall peptidoglycan (PG) analogues are reported herein. The Cpl-1 structure is folded in two well defined modules, one responsible for anchoring to the pneumococcal cell wall and the other, a catalytic module, that hydrolyzes the PG. Conformational rearrangement of Tyr-127 is a critical event in molecular recognition of a stretch of five saccharide rings of the polymeric peptidoglycan (cell wall). The PG is bound at a stretch of the surface that is defined as the peptidoglycan-binding sites 1 and 2, the juncture of which catalysis takes place. The peptidoglycan-binding site 1 binds to a stretch of three saccharides of the peptidoglycan in a conformation essentially identical to that of the peptidoglycan in solution. In contrast, binding of two peptidoglycan saccharides at the peptidoglycan-binding site 2 introduces a kink into the solution structure of the peptidoglycan, en route to catalytic turnover. These findings provide the first structural evidence on recognition of the peptidoglycan and shed light on the discrete events of cell wall degradation by Cpl-1.

Selected figure(s)

Figure 1.
FIGURE 1. Schematic drawing of the three peptidoglycan analogues bound to Cpl-1. 2S2P is disaccharide-dipeptide, 2S5P is disaccharide-pentapeptide, and (2S5P)[2] is tetrasaccharide-di-pentapeptide.

Figure 4.
FIGURE 4. Details of peptidoglycan recognition by Cpl-1. A, superimposition of the crystallographic coordinates for Cpl-1[E94Q]-(2S5P)[2] (in white) with the computational model for Cpl-1-(2S5P)[3] (in black). The computational model traces the crystallographically determined portions of the structure but also provides information on the portions of the structure of the ligand that did not appear in the crystallographic data. Regions involved in substrate recognition are highlighted in pink for PGBS1, and in blue for PGBS2. The catalytic residues Glu-94 and Asp-10 are in orange. B, stereo view of the crystallographic complex Cpl-1[E94Q]-(2S5P)[2] showing the interactions between Cpl-1 and (2S5P)[2]. Carbon atoms of the ligand are in green, and the two catalytic residues are highlighted in orange. Hydrogen bonds are shown as dashed lines. C, stereo view representation of the interactions in Cpl-1-(2S5P)[3] with the PG at positions -2to +3. Ligand and catalytic residues are in green and orange, respectively, and the formate anion is in cyan.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 24990-24999) copyright 2007.

Figures were selected by the author.

Author's comment

The knowledge of the molecular and structural basis for cell wall recognition by endolysins (bacteriophage encoded lysins) is key to understand how the bacterial envelope is degraded by endolysins,and also shed light on the function and improvement of enzybiotics. In Cpl-1 the PG is bound to a region of the protein surface that was defined as the PG-binding sites 1 and 2 at whose juncture catalysis takes place. The PG-binding site 1 binds to three saccharides in a conformation essentially identical to that observed for the PG in solution. In contrast, binding of two saccharides at the PG-binding site 2 introduces a kink in the PG, as observed in the solution structure and this may contribute to catalysis.