PDBsum entry 3cgn

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Isomerase PDB id
Protein chain
151 a.a. *
Waters ×21
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of thermophilic slyd
Structure: Peptidyl-prolyl cis-trans isomerase. Chain: a. Synonym: slyd. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.70Å     R-factor:   0.209     R-free:   0.257
Authors: P.Neumann,C.Loew,M.T.Stubbs,J.Balbach
Key ref: C.Löw et al. (2010). Crystal structure determination and functional characterization of the metallochaperone SlyD from Thermus thermophilus. J Mol Biol, 398, 375-390. PubMed id: 20230833 DOI: 10.1016/j.jmb.2010.03.014
06-Mar-08     Release date:   10-Mar-09    
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Protein chain
Pfam   ArchSchema ?
Q5SLE7  (Q5SLE7_THET8) -  Peptidyl-prolyl cis-trans isomerase
149 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein folding   2 terms 
  Biochemical function     isomerase activity     3 terms  


    Added reference    
DOI no: 10.1016/j.jmb.2010.03.014 J Mol Biol 398:375-390 (2010)
PubMed id: 20230833  
Crystal structure determination and functional characterization of the metallochaperone SlyD from Thermus thermophilus.
C.Löw, P.Neumann, H.Tidow, U.Weininger, C.Haupt, B.Friedrich-Epler, C.Scholz, M.T.Stubbs, J.Balbach.
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.