JMol Tutorial created with support from Dr. Vincent Fischetti (Fischetti Lab, Rockefeller University) and Tim Herman (Center for Biomolecular Modeling).

Please email tshata@gmail.com if you have any questions or to report problems with this tutorial.  Thank you.

Using this tutorial:
This website runs the Jmol molecule viewer. You will need a Java-enabled browser to view this website. Refresh your browser to resize applet to your screen size.

You can follow the tutorial below while watching short animated scripts by clicking the appropriate buttons.  At anytime, if you want to change the view of the structure, do the following:
Rotate: Click on mouse and drag
Zoom: Scroll wheel on your mouse or +Shift and left click
Move: +Ctrl and right click

If you are familiar with RasMol commands, you can also use them through the JMol console.

 

 

 

 

Introduction

PlyB is a lysin active against the Bacillus anthracis-like strain ATCC 4342. Lysins are peptidoglycan hydrolases used by bacteriophage (phage) to cleave covalent crosslinks in the host cell wall.  The compromised cell wall leads to host cell lysis, releasing the progeny phage.

The growing concern for community-acquired multi-drug-resistant bacteria and the intentional engineering of multi-resistant strains for biological weapons make new antibacterial drugs necessary.  Phage encoded lysins have characteristics making them favorable candidates for novel antibacterial drugs. 

PlyB is encoded by a single gene and contains a distinct catalytic domain (PlyBcat) and a binding-domain.  The structure of PlyBcat is explored in this tutorial.

PlyBcat has a distinctive β/α-barrel fold structure ceomposed of 7 parallel β-strands (teal), a single anti-parallel β-strand (purple), and 5 α-helics (orange). The enzyme's active site is located at the base of this barrel structure, which forms a characteristic groove that can be highlighted by viewing the structure in "spacefill" (see scripts below).
 

Highlight residues involved in enzyme activity

The four residues seen here are Asp6, Asp90, Glu92 and Asp171. Positioned along the rim of the cavity formed at one end of the β/α-barrel, they act as the catalytic machinery in the active site of PlyBcat. It has been suggested that Asp6 and Glu92 perform an acid/base catalytic mechanism, which donates a proton to the substrate sugar, creating a net inversion of the anomeric center of the sugar.

Asp90 and Asp171 form hydrogen bonds with Asp6 and Glu92 respectively, allowing the transfer of a proton from one residue to the other, regenerating Asp6 and Glu92 to their original protonated state.
Asp6 and Glu92 (catalytic residues, colored orange)

Asp90 and Asp171 (colored green)


Viewing protein in spacefill; highlighting the active site

The blue section seen in this view shows the negatively charged active site of PlyBcat. Composed of the amino acids Tyr58, Phe60, Val88, Trp141, Tyr121, Ile27, Asp6, Asp90, Glu92 and Asp171, the active site is located towards the C-terminal direction of the parallel β-sheets. The four acidic residues (Asp6, Asp90, Glu92 and Asp171) are the key catalytic residues in the active site (see script above).  The orange residues seen here, Tyr145, Glu160, Tyr161, Lys169, Gly168, Trp10, ARg29, Asp32, Phe60, Glu92, Gly123, His124 and His125, line the groove around the active site to form the substrate binding site.

 

Model Designs

Wireframe model
protein backbone 300, amino acid sidechains wireframe 250.
sidechains on Asp6, Glu92, Asp90, and Asp171 shown.

Spacefill model
spacefill 375

 

Tutorial and scripts prepared by Danielle Cosentino, Calvin Jones, and Becky Krakora

PDB File: 2NW0

Reference: Porter, C.J., Schuch, R., Pelzek, A.J., Buckle, A.M., McGowan, S., Wilce, M.C., Rossjohn, J., Russell, R., Nelson, D., Fischetti, V.A., Whisstock, J.C. (2007) The 1.6 A Crystal Structure of the Catalytic Domain of PlyB, a Bacteriophage Lysin Active Against Bacillus anthracis. J.Mol.Biol. 366: 540-550