4JJM

Structure of a cyclophilin from Citrus sinensis (CsCyp) in complex with cyclosporin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A redox 2-cys mechanism regulates the catalytic activity of divergent cyclophilins.

Campos, B.M.Sforca, M.L.Ambrosio, A.L.Domingues, M.N.Brasil de Souza Tde, A.Barbosa, J.A.R.G.Paes Leme, A.F.Perez, C.A.Whittaker, S.B.Murakami, M.T.Zeri, A.C.Benedetti, C.E.

(2013) Plant Physiol. 162: 1311-1323

  • DOI: 10.1104/pp.113.218339

  • PubMed Abstract: 
  • The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA pol ...

    The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.


    Organizational Affiliation

    Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase
A, B
175Citrus sinensisMutation(s): 0 
Gene Names: CYP
EC: 5.2.1.8
Find proteins for D0ELH5 (Citrus sinensis)
Go to UniProtKB:  D0ELH5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cyclosporin A
E, F
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
E,FCyclosporin ACyclic peptide / Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.630α = 90.00
b = 83.630β = 90.00
c = 85.030γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Database references
  • Version 1.3: 2018-12-05
    Type: Data collection, Structure summary