Structural and mechanistic analysis of two prolyl endopeptidases: Role of interdomain dynamics in catalysis and specificity

Shan et al. 10.1073/pnas.0408286102.

Supporting Information

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Supporting Figure 5
Supporting Figure 6
Supporting Figure 7
Supporting Figure 8

Supporting Figure 5

Fig. 5. Electron density maps (2F_o – F_c, contoured at 1s level) for residues in the disallowed regions of the Ramachandran plot for MX PEP and SC PEP. (A) K341 in SC PEP. (B) Q295 in MX PEP (monomer A). (C) Q295 in MX PEP (monomer B). (D) Active site S575 in SC PEP. (E) Active site S533 in MX PEP (monomer A). (F) Active site S533 in MX PEP (monomer B).

Supporting Figure 6

Fig. 6. Top view of the catalytic domain of MX PEP. The numbering convention of the secondary structures was as described in Fulop, V., Bocskei, Z. & Polgar, L. (1998) Cell 94, 161–170. The catalytic triad residues are S533 (magenta), D616 (blue), and H651 (gray).

Supporting Figure 7

Fig. 7. Structural alignment of MX and SC PEPs. MX PEP, blue; SC PEP, purple. (Left) MX and SC proteins aligned at their catalytic domains. (Right) Propeller domain alignment. Structural variations come mainly from the loops between the b -strands, with examples labeled in black. The arrows (magenta) point to the loops that have become unstructured in the open form.

Supporting Figure 8

Fig. 8. Sequence alignment of prolyl-specific peptidases. PEPs from Myxococcus xanthus (MX), Sphingomonas capsulata (SC), porcine muscle (porcine), and Flavabacterium meningosepticum (FM), and a prolyl-specific exopeptidase dipeptidyl peptidase (DPPIV) are aligned. The high-consensus residues are highlighted in red, and low-consensus residues are highlighted in blue.