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.
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.
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.
has a distinctive β/α-barrel
fold structure ceomposed of 7 parallel
(teal), a single
(purple), and 5
(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
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
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.
Asp171 form hydrogen bonds with
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
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
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.
protein backbone 300, amino acid sidechains wireframe 250.
sidechains on Asp6, Glu92, Asp90, and Asp171 shown.
Tutorial and scripts prepared by Danielle Cosentino, Calvin Jones,
and Becky Krakora