PDBsum entry 2c3b

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Isomerase PDB id
Protein chains
141 a.a. *
SO4 ×2
Waters ×123
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: The crystal structure of aspergillus fumigatus cyclophilin reveals 3d domain swapping of a central element
Structure: Ppiase. Chain: a, b. Synonym: cyclophilin. Engineered: yes
Source: Aspergillus fumigatus. Organism_taxid: 5085. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.85Å     R-factor:   0.191     R-free:   0.214
Authors: A.Limacher,D.P.Kloer,S.Fluckiger,G.Folkers,R.Crameri, L.Scap
Key ref:
A.Limacher et al. (2006). The Crystal Structure of Aspergillus fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element. Structure, 14, 185-195. PubMed id: 16472738 DOI: 10.1016/j.str.2005.10.015
05-Oct-05     Release date:   30-Jan-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q4WHY9  (Q4WHY9_ASPFU) -  Peptidyl-prolyl cis-trans isomerase
205 a.a.
141 a.a.
Key:    PfamA domain  Secondary structure

 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   1 term 
  Biochemical function     peptidyl-prolyl cis-trans isomerase activity     1 term  


    Added reference    
DOI no: 10.1016/j.str.2005.10.015 Structure 14:185-195 (2006)
PubMed id: 16472738  
The Crystal Structure of Aspergillus fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element.
A.Limacher, D.P.Kloer, S.Flückiger, G.Folkers, R.Crameri, L.Scapozza.
The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.
  Selected figure(s)  
Figure 3.
Figure 3. W Loop Bound to Active Site and Second Hinge Loop
(A) Electron density of the second hinge loop and parts of the adjacent W loop (aa 124-129). The experimental map is contoured at 1s using solvent-flattened experimental phases calculated without NCS averaging. H bonds within and between the hinges of both chains are indicated by yellow, dashed lines. Residues of chain A and B are colored in violet and green, respectively.
(B) Hydrophobic binding of the W loop into its own active site. Trp124 and Leu125 of chain A sit into the hydrophobic pocket of subunit A, making hydrophobic interactions with surrounding residues of both chains. In subunit B, Val121 and Trp124 of chain B sit into its active site. Position and conformation of some distinctive residues of human CyPA (2CPL) are shown for comparison. Two independent monomers of CyPA were superimposed on either subunit of Asp f 11 (see Figure 1C). Side chains of CyPA superposed on subunit A and B are colored in orange and yellow, respectively.
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 185-195) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18065652 J.Stie, and D.Fox (2008).
Calcineurin regulation in fungi and beyond.
  Eukaryot Cell, 7, 177-186.  
18342330 V.Thai, P.Renesto, C.A.Fowler, D.J.Brown, T.Davis, W.Gu, D.D.Pollock, D.Kern, D.Raoult, and E.Z.Eisenmesser (2008).
Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.
  J Mol Biol, 378, 71-86.
PDB code: 2ose
17698001 Y.Hirano, M.M.Hossain, K.Takeda, H.Tokuda, and K.Miki (2007).
Structural studies of the Cpx pathway activator NlpE on the outer membrane of Escherichia coli.
  Structure, 15, 963-976.
PDB codes: 2z4h 2z4i
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