Serine Proteases Part 4

Index to Course Material Index to Section 12 Enzymes Index; Part 3 Part 5

Summary of highlighted residues in chymotrypsin

                                                   in loop
                                                   between   colour in
                                          domain   strands:  diagrams
                                          ______   ________  _________

Catalytic Triad        His-57  side chain   1          3,4      red
                       Asp-102 side chain   1          5,6
                       Ser-195 side chain   2          3,4

Oxyanion Hole          Gly-193 main chain   2          3,4      white
                       Ser-195 main chain   2          3,4

Specificity Pocket     Ser-189 side chain   2          5,6      green
                       Gly-216 side chain   2          5,6
                       Gly-226 side chain   2          3,4
                               

Main Chain             Ser-214 main chain   2          5,6      yellow
   Substrate Binding   Trp-215 main chain   2          5,6
                       Gly-216 main chain   2          5,6

Tripeptide cleavage                                             blue
   product

The following diagrams are of chymotrypsin complexed with a tripeptide (crystal structure 8gch).

If you have not already done so, load the 8gch structure into RasMol.

8gch (185Kb) [Bbk|BNL|ExP|Waw|Hal]

SCRIPT 1 (also on the previous page) highlights the residues of interest with the colour scheme described. It defines the following RasMol sets:

• triad - the catalytic triad
• oxyhole - the oxyanion hole
• pocket - the principal residues of the substrate-binding pocket
• allpocket - other residues of the substrate-binding pocket
• hydbond - the backbone groups which hydrogen bond to the substrate

These sets can be turned on and off with the commands:

select <name of set>
wireframe 80 (to switch on)
wireframe off (to switch off)

The tripeptide (Gly-Ala-Trp) is in fact a product of autolysis, i.e. a peptide fragment produced by the hydrolysis of chymotrypsin by another chymotrypsin molecule; refer to Part 1 . The large tryptophan side chain is situated inside the specificity pocket.

(Crystallography note: numerous different types of peptide fragment occurred in different chymotrypsin molecules in the protein crystal; this tripeptide results from the overlapping electron density of different asymmetric units.)

Views are shown both with and without the tripeptide fragment.

A view looking into the substrate-specificity pocket, without tripeptide:

close up

If you have already applied SCRIPT 1, you can obtain a similar view by cutting and pasting the following commands:

• reset
• rotate z -29
• rotate y -4
• rotate x 86
• translate y 30
• zoom 250

The same view with tripeptide:

close up

To switch on the tripeptide (chain C in the crystal structure), simply use the following commands:

• select *c
• wireframe 100
• colour blue

• select trp252c.C
• spacefill 200

A different view to illustrate the main-chain hydrogen bonding to the substrate/product.

This view may be obtained with the commands:

• reset
• rotate z -75
• rotate y -15
• rotate x 90
• translate x 3
• translate y 30
• zoom 255

To highlight the groups involved in the enzyme-substrate hydrogen bonding:

• select ser214.O,gly216.N,gly216.O,gly250.N,gly250.O,trp252.N
• dots 500

SCRIPT 3 displays, from scratch, all the residues of interest and the tripeptide highlighting enzyme-substrate binding.

Other useful renditions are those with the enzyme and product as spacefill and wireframe respectively (or vice versa); e.g. select protein and not *c. followed by spacefill.

102Kb GIF

Index to Course Material

Index to Section 12

Enzymes Index

Part 3

Part 5

Last updated 11th Jul '96