The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile

Bradshaw, W.J.; Kirby, J.M.; Thiyagarajan, N.; Chambers, C.J.; Davies, A.H.; Roberts, A.K.; Shone, C.C.; Acharya, K.R.

doi:10.1107/S1399004714009997

Figure 3
Cysteine protease propeptide and active-site groove. (a) The full length of the propeptide from His33 to Lys91 shown with sticks, ribbon and electron density (1σ, 2F_o − F_c map). The novel fold of the 30 residues is shown at the bottom of the image, while the normal section within the active-site groove is shown at the top of the image. Poor density that allowed modelling of Gly58–Tyr63 with a fair level of confidence can be observed on the right, and a lack of density for the unmodelled section towards the end of the propeptide is shown at the top. (b, c) Molecular surface of the cysteine protease active-site groove containing the propeptide; the two images are 50° apart. As in Fig. 1

(a), the cysteine protease domain is shown in green and the lectin-like domain is shown in cyan; the three active-site residues are shown in pink. Propeptide residues before Asn64 have been removed for clarity. Met73 shows multiple conformations. Owing to the proximity of the side-chain carbonyl of Asn114 and the backbone carbonyl of Asn261 (4.7 Å in chain A and 4.6 Å in chain B), a continuous section of surface is shown above the active site. The propeptide fills the active-site groove and is shown in close contact with both domains. (d) Active site of Cwp84, with catalytic residues, residues involved in the formation of the S₂ negatively charged pocket and Val66 from the propeptide shown. The negatively charged S₂ pocket is shown surrounded by the residues that form it: Ser235, which shows multiple conformations, Thr317, Asp318 and Asp320. Note that Val66 does not enter the negatively charged pocket, but we propose that the P₂ lysine of SlpA would. The oxyanion hole, formed by Gln110 and Cys116Ala, which stabilizes a catalytic intermediate, is also visible on the left. (e) Occlusion of the active-site residues by Asn114 and Asn261. We propose that their proximity to each other is a result of interactions with the propeptide and assists in the prevention of binding of the substrate. Upon removal of the propeptide, the distance may be lengthened slightly, opening the active site.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 70| Part 7| July 2014| Pages 1983-1993

https://doi.org/10.1107/S1399004714009997

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