Another example of protein function - Lysozyme

In particular, hen egg white lysozyme (HEWL)

Size:  14.6 kD, 129 aa’s.

Function  

• Destruction of bacterial (and fungi) cell walls.

• Through hydrolysis of glycosidic linkages.

• HEWL rate ~108 faster than non-catalysed hydrolysis

• Found widely in vertebrates

• Possible role in bacteriocidal action.

• More likely role in ‘cleaning away’ dead bacteria.

Underlying chemistry

• Gram-positive bacteria have crosslinked peptidoglycan cell walls.

• The oligosaccharide is an alternating arrangement of two saccharide subunits

• 2-acetamido-2-deoxyglucopyranoside (NAG)

• 2-acetamido-2-deoxy-3-O-lactylglucopyranoside (NAM)

NAG and NAM are b(1  4)-linked.  
Many fungi cell walls contain chitin, which is b(1 4)-linked poly(NAG).

(For definition of b configuration of saccharides, see section 1.2.7)

So the chemistry is the cleavage of one of the etheric bonds of an acetal, forming a hemiacetal.
When this type of hydrolysis is undertaken in the lab, the reaction results from treatment with a dilute mineral acid.
Of course, with most acetals the reaction would proceed back through the hemiacetal, giving the aldehyde as the final product.
An acid catalysed acetal hydrolysis has an SN1-like mechanism.
 
HEWL Catalytic strategy
• HEWL uses two key residues in the catalytic mechanism
• Glu 35 – acid and base catalysis, proximity/orientation of hydrolysing water molecule.
• Asp 52 – covalent catalysis
 
Mechanism and structure
• Two previously proposed mechanisms.
• Recent crystallographic results (Vocaldo et al, Nature, 2000, 412 (23rd August issue), 835-838) 
demonstrate the mechanism shown below.
• This is different than the "Phillips mechanism" in most text books!
Look through the mechanism below and identify which of the common enzyme catalytic 
strategies are being used.
• Acid base catalysis
• Electrostatic interactions
• Covalent catalysis (intermediate formation) 
• Proximity and orientation effects
• Strain
• Changes in reaction conditions.
 
Please note that the saccharide subunits in the following mechanism are highly simplified!

 

Note that the main movement in this mechanism is at C1 of the subunit that becomes attached to Asp 52.  This undergoes movement as the residue converts between boat and chair conformations.

 

Lysozyme with a saccharide mimic bound to Asp 52 (from Nature, 2000, 412 (23rd August issue), 835-838, crystal structure in protein database, file 1h6m.pdb).

Click picture for larger version

 

This is also available as an interactive model