Crystal Structure of thermophilic SlyD

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus

Loew, C.Neumann, P.Tidow, H.Weininger, U.Haupt, C.Friedrich-Epler, B.Scholz, C.Stubbs, M.T.Balbach, J.

(2010) J Mol Biol 398: 375-390

  • DOI: https://doi.org/10.1016/j.jmb.2010.03.014
  • Primary Citation of Related Structures:  
    3CGM, 3CGN, 3LUO

  • PubMed Abstract: 

    SlyD (sensitive to lysis D; product of the slyD gene) is a prolyl isomerase [peptidyl-prolyl cis/trans isomerase (PPIase)] of the FK506 binding protein (FKBP) type with chaperone properties. X-ray structures derived from three different crystal forms reveal that SlyD from Thermus thermophilus consists of two domains representing two functional units. PPIase activity is located in a typical FKBP domain, whereas chaperone function is associated with the autonomously folded insert-in-flap (IF) domain. The two isolated domains are stable and functional in solution, but the presence of the IF domain increases the PPIase catalytic efficiency of the FKBP domain by 2 orders of magnitude, suggesting that the two domains act synergistically to assist the folding of polypeptide chains. The substrate binding surface of SlyD from T. thermophilus was mapped by NMR chemical shift perturbations to hydrophobic residues of the IF domain, which exhibits significantly reduced thermodynamic stability according to NMR hydrogen/deuterium exchange and fluorescence equilibrium transition experiments. Based on structural homologies, we hypothesize that this is due to the absence of a stabilizing beta-strand, suggesting in turn a mechanism for chaperone activity by 'donor-strand complementation.' Furthermore, we identified a conserved metal (Ni(2+)) binding site at the C-terminal SlyD-specific helical appendix of the FKBP domain, which may play a role in metalloprotein assembly.

  • Organizational Affiliation

    Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase158Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q5SLE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLE7 
Go to UniProtKB:  Q5SLE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLE7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.18α = 90
b = 85.09β = 90
c = 92.22γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description