Skip to main content
Fig. 5 | BMC Biology

Fig. 5

From: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD

Fig. 5

Binding of peptides and FK506 to the FK506-binding protein (FKBP) domain. a The substrate-free FKBP domain of TtSlyDFL:S2-plus2. The color scheme is the same as used in Fig. 2, except that residues 62–64 are violet, and the residues forming the hydrophobic binding pocket are green. Residues involved in binding are shown in sticks. b Binding of FK506 to full-length TtSlyD (TtSlyDFL). Dashes indicate distances up to 3.5 Å between conventional hydrogen bond donors and acceptors (weaker bonds such as CH–O and CH–π are omitted). The pipecolinyl ring and selected atoms of FK506 are labeled. c Binding of the S2-W23A peptide to molecule A in TtSlyDFL:S2-W23A. A similar binding mode is also seen for molecule C and TtSlyDFL:S2. For clarity, side chains are only shown for residues 27–29 of the peptide. The residues of the peptide are labeled. d Binding of the S2-W23A peptide to molecule D in TtSlyDFL:S2-W23A. A similar binding mode is also seen for molecule B and TtSlyDΔIF:S2-W23A. e Ramachandran plots for residues K28S2 and P29S2 of TtSlyDFL:S2 as well as TtSlyDFL:S2-W23A molecules A and C compared to the standard values for i + 1 and i + 2 residues of a type VIa1 β-turn. There is a clear match. f Similar Ramachandran plots for residues K28S2 and P29S2 of TtSlyDFL:S2-W23A molecules B and D as well as TtSlyDΔIF:S2W23-A compared to the standard values of a type VIb β-turn. There is a partial match, but the phi angle of K28S2 (position i + 1) is off by 40–60°. Additional file 7 shows an analysis of the structural changes in the FKBP domain induced by substrate binding, Additional file 8 illustrates the non-canonical binding modes of the T1 and S3 peptides, and Additional file 9 shows the peripheral substrate:FKBP domain interactions

Back to article page