4ODM: Structure Of Slyd From Thermus Thermophilus In Complex With S2-w23a Peptide

Citation:
Abstract
BACKGROUND: Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD is a two-domain enzyme containing both a PPIase FK506-binding protein (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the FKBP domain being limited to complexes involving various inhibitor compounds or a chemically modified tetrapeptide. RESULTS: We have characterized the binding of 15-residue-long unmodified peptides to SlyD from Thermus thermophilus (TtSlyD) in terms of binding thermodynamics and enzyme kinetics through the use of isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, and site-directed mutagenesis. We show that the affinities and enzymatic activity of TtSlyD towards these peptides are much higher than for the chemically modified tetrapeptides that are typically used for activity measurements on FKBPs. In addition, we present a series of crystal structures of TtSlyD with the inhibitor FK506 bound to the FKBP domain, and with 15-residue-long peptides bound to either one or both domains, which reveals that substrates bind in a highly adaptable fashion to the IF domain through beta-strand augmentation, and can bind to the FKBP domain as both types VIa1 and VIb-like cis-proline beta-turns. Our results furthermore provide important clues to the catalytic mechanism and support the notion of inter-domain cross talk. CONCLUSIONS: We found that 15-residue-long unmodified peptides can serve as better substrate mimics for the IF and FKBP domains than chemically modified tetrapeptides. We furthermore show how such peptides are recognized by each of these domains in TtSlyD, and propose a novel general model for the catalytic mechanism of FKBPs that involves C-terminal rotation around the peptidyl-prolyl bond mediated by stabilization of the twisted transition state in the hydrophobic binding site.
PDB ID: 4ODMDownload
MMDB ID: 126017
PDB Deposition Date: 2014/1/10
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 1.75  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Biological Unit for 4ODM: trimeric; determined by author
Molecular Components in 4ODM
Label Count Molecule
Proteins (3 molecules)
1
Peptidyl-prolyl Cis-trans Isomerase Slyd
Molecule annotation
2
30S Ribosomal Protein S2(Gene symbol: rpsB)
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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