PDBsum entry: 1xov

Hydrolase

PDB id: 1xov

Contents

Protein chain

315 a.a. *

Ligands

SO4

GLU-LYS

TRS

Metals

_ZN

_CL

Waters ×307

* Residue conservation analysis

PDB id:

1xov

Name:

Hydrolase

Title:

The crystal structure of the listeria monocytogenes bacterio endolysin plypsa

Structure:

Ply protein. Chain: a. Synonym: plypsa. Engineered: yes

Source:

Listeria phage psa. Organism_taxid: 171618. Gene: ply. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: host: listeria monocytogenes

Resolution:

1.80Å R-factor: 0.172 R-free: 0.198

Authors:

I.P.Korndoerfer,A.Skerra

Key ref:

I.P.Korndörfer et al. (2006). The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls. J Mol Biol, 364, 678-689. PubMed id: 17010991 DOI: 10.1016/j.jmb.2006.08.069

Date:

07-Oct-04 Release date: 18-Oct-05

Protein chain

Q8W5Y8  (Q8W5Y8_9CAUD) -  Ply protein

Seq: 314 a.a.

Struc: 315 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: peptidoglycan catabolic process (1 term)
• Biochemical function: metal ion binding (2 terms)

DOI no: 10.1016/j.jmb.2006.08.069

J Mol Biol 364:678-689 (2006)

PubMed id: 17010991

The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls.

I.P.Korndörfer, J.Danzer, M.Schmelcher, M.Zimmer, A.Skerra, M.J.Loessner.

ABSTRACT

Bacteriophage murein hydrolases exhibit high specificity towards the cell walls of their host bacteria. This specificity is mostly provided by a structurally well defined cell wall-binding domain that attaches the enzyme to its solid substrate. To gain deeper insight into this mechanism we have crystallized the complete 314 amino acid endolysin from the temperate Listeria monocytogenes phage PSA. The crystal structure of PlyPSA was determined by single wavelength anomalous dispersion methods and refined to 1.8 A resolution. The two functional domains of the polypeptide, providing cell wall-binding and enzymatic activities, can be clearly distinguished and are connected via a linker segment of six amino acid residues. The core of the N-acetylmuramoyl-L-alanine amidase moiety is formed by a twisted, six-stranded beta-sheet flanked by six helices. Although the catalytic domain is unique among the known Listeria phage endolysins, its structure is highly similar to known phosphorylase/hydrolase-like alpha/beta-proteins, including an autolysin amidase from Paenibacillus polymyxa. In contrast, the C-terminal domain of PlyPSA features a novel fold, comprising two copies of a beta-barrel-like motif, which are held together by means of swapped beta-strands. The architecture of the enzyme with its two separate domains explains its unique substrate recognition properties and also provides insight into the lytic mechanisms of related Listeria phage endolysins, a class of enzymes that bear biotechnological potential.

Selected figure(s)

Figure 3.
Figure 3. Crystal structure of PlyPSA. The EAD is shown in blue, the linker region in grey, and the CBD in red. The catalytic Zn^2+ is depicted as a yellow sphere. Figure 3. Crystal structure of PlyPSA. The EAD is shown in blue, the linker region in grey, and the CBD in red. The catalytic Zn^2+ is depicted as a yellow sphere.

Figure 8.
Figure 8. Architecture and putative ligand-binding sites of the PlyPSA CBD. (a) Organisation of its two subdomains. Proximal and distal subdomain of the CBD are coloured in orange and red, respectively, except for the structurally swapped strands, which are coloured according to their sequential neighbourhood (see also Figure 1). (b) Superposition of the proximal and distal subdomains (coloured as in (a)). (c) Schematic representation of the ancestral CBD subdomain. (d) Distribution of aromatic side-chains in the CBD and indication of a putative binding site. Residues with uncharged aromatic side-chains are shown as green stick models (backbone coloured as in (a)). (e) Surface representation of the CBD with hydrophobic surface areas coloured in green (as described^53). The white ellipsoid indicates the location of a cleft between the two subdomains that may be suited to bind cell wall associated ligands. Figure 8. Architecture and putative ligand-binding sites of the PlyPSA CBD. (a) Organisation of its two subdomains. Proximal and distal subdomain of the CBD are coloured in orange and red, respectively, except for the structurally swapped strands, which are coloured according to their sequential neighbourhood (see also [3]Figure 1). (b) Superposition of the proximal and distal subdomains (coloured as in (a)). (c) Schematic representation of the ancestral CBD subdomain. (d) Distribution of aromatic side-chains in the CBD and indication of a putative binding site. Residues with uncharged aromatic side-chains are shown as green stick models (backbone coloured as in (a)). (e) Surface representation of the CBD with hydrophobic surface areas coloured in green (as described[4]^53). The white ellipsoid indicates the location of a cleft between the two subdomains that may be suited to bind cell wall associated ligands.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 678-689) copyright 2006.

Figures were selected by the author.