PDBsum entry 3rfy

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protein links
Isomerase PDB id
Jmol PyMol
Protein chain
356 a.a.
Waters ×114
PDB id:
Name: Isomerase
Title: Crystal structure of arabidopsis thaliana cyclophilin 38 (at
Structure: Peptidyl-prolyl cis-trans isomerase cyp38, chloro chain: a. Synonym: ppiase cyp38, rotamase cyp38, thylakoid lumen ppia engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: at3g01480, cyp38, f4p13.3. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.39Å     R-factor:   0.248     R-free:   0.266
Authors: D.Vasudevan,K.Swaminathan
Key ref: D.Vasudevan et al. (2012). Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism. Plant Cell, 24, 2666-2674. PubMed id: 22706283 DOI: 10.1105/tpc.111.093781
07-Apr-11     Release date:   13-Jun-12    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9SSA5  (CYP38_ARATH) -  Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
437 a.a.
356 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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     peptidyl-prolyl cis-trans isomerase activity     1 term  


    Added reference    
DOI no: 10.1105/tpc.111.093781 Plant Cell 24:2666-2674 (2012)
PubMed id: 22706283  
Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism.
D.Vasudevan, A.Fu, S.Luan, K.Swaminathan.
Cyclophilin38 (CYP38) is one of the highly divergent cyclophilins from Arabidopsis thaliana. Here, we report the crystal structure of the At-CYP38 protein (residues 83 to 437 of 437 amino acids) at 2.39-Å resolution. The structure reveals two distinct domains: an N-terminal helical bundle and a C-terminal cyclophilin β-barrel, connected by an acidic loop. Two N-terminal β-strands become part of the C-terminal cyclophilin β-barrel, thereby making a previously undiscovered domain organization. This study shows that CYP38 does not possess peptidyl-prolyl cis/trans isomerase activity and identifies a possible interaction of CYP38 with the E-loop of chlorophyll protein47 (CP47), a component of photosystem II. The interaction of CYP38 with the E-loop of CP47 is mediated through its cyclophilin domain. The N-terminal helical domain is closely packed together with the putative C-terminal cyclophilin domain and establishes a strong intramolecular interaction, thereby preventing the access of the cyclophilin domain to other proteins. This was further verified by protein-protein interaction assays using the yeast two-hybrid system. Furthermore, the non-Leucine zipper N-terminal helical bundle contains several new elements for protein-protein interaction that may be of functional significance. Together, this study provides the structure of a plant cyclophilin and explains a possible mechanism for autoinhibition of its function through an intramolecular interaction.