3LUO

Crystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD

Summary for 3LUO

• Entry DOI: 10.2210/pdb3luo/pdb
• Related: 3CGM 3CGN
• Descriptor: Peptidyl-prolyl cis-trans isomerase, Suc-Ala-Leu-Pro-Phe-pNA, ZINC ION, ... (4 entities in total)
• Functional Keywords: prolyl cis trans isomerase, chaperone function, two domain protein, ni(2+) zn(2+) binding, slyd, isomerase
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 2
• Total formula weight: 18252.49

Authors

Loew, C.,Neumann, P.,Weininger, U.,Stubbs, M.T.,Balbach, J. (deposition date: 2010-02-18, release date: 2010-03-31, Last modification date: 2023-11-01)

Primary citation

Loew, C.,Neumann, P.,Tidow, H.,Weininger, U.,Haupt, C.,Friedrich-Epler, B.,Scholz, C.,Stubbs, M.T.,Balbach, J.
Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus
J.Mol.Biol., 398:375-390, 2010

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.

PubMed: 20230833
DOI: 10.1016/j.jmb.2010.03.014

Experimental method

X-RAY DIFFRACTION (2.55 Å)