4HY7

Structural and biochemical characterization of a cytosolic wheat cyclophilin TaCypA-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and biochemical characterization of the cytosolic wheat cyclophilin TaCypA-1.

Sekhon, S.S.Kaur, H.Dutta, T.Singh, K.Kumari, S.Kang, S.Park, S.G.Park, B.C.Jeong, D.G.Pareek, A.Woo, E.J.Singh, P.Yoon, T.S.

(2013) Acta Crystallogr.,Sect.D 69: 555-563

  • DOI: 10.1107/S0907444912051529
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclophilins belong to a family of proteins that bind to the immunosuppressive drug cyclosporin A (CsA). Several members of this protein family catalyze the cis-trans isomerization of peptide bonds preceding prolyl residues. The present study describ ...

    Cyclophilins belong to a family of proteins that bind to the immunosuppressive drug cyclosporin A (CsA). Several members of this protein family catalyze the cis-trans isomerization of peptide bonds preceding prolyl residues. The present study describes the biochemical and structural characteristics of a cytosolic cyclophilin (TaCypA-1) cloned from wheat (Triticum aestivum L.). Purified TaCypA-1 expressed in Escherichia coli showed peptidyl-prolyl cis-trans isomerase activity, which was inhibited by CsA with an inhibition constant of 78.3 nM. The specific activity and catalytic efficiency (kcat/Km) of the purified TaCypA-1 were 99.06 ± 0.13 nmol s(-1) mg(-1) and 2.32 × 10(5) M(-1) s(-1), respectively. The structures of apo TaCypA-1 and the TaCypA-1-CsA complex were determined at 1.25 and 1.20 Å resolution, respectively, using X-ray diffraction. Binding of CsA to the active site of TaCypA-1 did not result in any significant conformational change in the apo TaCypA-1 structure. This is consistent with the crystal structure of the human cyclophilin D-CsA complex reported at 0.96 Å resolution. The TaCypA-1 structure revealed the presence of a divergent loop of seven amino acids (48)KSGKPLH(54) which is a characteristic feature of plant cyclophilins. This study is the first to elucidate the structure of an enzymatically active plant cyclophilin which shows peptidyl-prolyl cis-trans isomerase activity and the presence of a divergent loop.


    Organizational Affiliation

    Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase
A
171Triticum aestivumMutation(s): 0 
Gene Names: CyP3 (CyP1, TaBWCyp A-1)
EC: 5.2.1.8
Find proteins for Q93W25 (Triticum aestivum)
Go to UniProtKB:  Q93W25
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclosporin A
B
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
BCyclosporin ACyclic peptide / Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.914α = 90.00
b = 49.847β = 90.00
c = 78.976γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references