Volume 4, Issue 10, Pages 1193-1203 (October 1996) The prosequence of procaricain forms an α-helical domain that prevents access to the substrate-binding cleft  Matthew R Groves, Mark AJ Taylor, Mandy Scott, Nicola J Cummings, Richard W Pickersgill, John A Jenkins  Structure  Volume 4, Issue 10, Pages 1193-1203 (October 1996) DOI: 10.1016/S0969-2126(96)00127-X

Figure 1 A sequence alignment of the proregions of caricain, papain and PPIV (now known as glycyl endopeptidase). Differences from the caricain sequence are highlighted in red. Secondary structure elements of procaricain are indicated; α helices in purple and β strands in yellow. Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 2 Ribbon representation of the secondary structure elements of procaricain. The three helices of the prodomain (blue) pack onto the mainly β sheet C-terminal domain of mature caricain (red). An extended polypeptide chain of the prodomain runs through the substrate-binding cleft between the C-terminal and N-terminal domains of mature caricain. (This figure was produced using the program QUANTA [Molecular Simulations Inc].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 3 Stereo diagram showing the Cα trace of procaricain. The prosequence is coloured red, the N-terminal domain of mature caricain is coloured in green and the C-terminal domain is in blue. (This figure was produced using the program O [23].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 4 Structural significance of the ERIFNIN motif. (a) A representation of the residues making up the ERIFNIN motif [15] on the core face of helix α2. Residues comprising the ERIFNIN motif are highlighted in red. Figure produced using the program O [23]. (b) Diagram showing the interactions made by residues within the ERIFNIN motif [15]. The prosequence structure is represented by green helices and red β strands; the blue helix is a portion of the mature sequence. A salt bridge is formed between Arg42p (helix α2) and Glu77p (helix α3) which stabilizes the packing of helices α2 and α3; this salt bridge is further stabilized by the presence of Glu38p. A salt bridge is also formed between the prodomain (Asp48p and Asn49p) and the C-terminal domain (Arg139) of procaricain. Hydrogen bonds are formed between Asn57p (helix α2) and the main chain of Leu65p, which is situated on the end of the β strand in the prodomain. This interaction stabilizes the packing of helix α2 and the β strand of the prodomain. (Figures produced using MOLSCRIPT [37] and RASTER3D [38].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 5 The packing of residues in the region of the P2′ pocket. This pocket provides a hydrophobic interface between the proregion and mature caricain. The electronic density is contoured at 1 σ. (Figure produced using the program O [23].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 6 Diagram indicating the temperature factors of the final procaricain model. Regions with lower temperature factors (B < 40 å2) are indicated by dark blue colouring, regions with the higher temperature factors are indicated in red. (Figure produced using rasmol [39].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)

Figure 7 A diagram showing the proregion as it passes through the substrate-binding cleft. The proregion is shown in ball-and-stick representation and caricain is depicted as a molecular surface representation; the most negative potentials are shown in red, the most positive are in blue. The position of Gly84p is indicated by the black arrow. The C-terminal domain of caricain is towards the top of the picture and the position of Asp158 is indicated. The surface is contoured at ± 12.5eV. (Figure produced using GRASP [40].) Structure 1996 4, 1193-1203DOI: (10.1016/S0969-2126(96)00127-X)