8B58 | pdb_00008b58

Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with Cyclosporin A

PDB DOI: https://doi.org/10.2210/pdb8B58/pdb

Classification: ISOMERASE
Organism(s): Toxoplasma gondii, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-22 Released: 2023-02-01
Deposition Author(s): Jimenez-Faraco, E., Hermoso, J.A.
Funding Organization(s): Agencia Estatal de Investigacion (AEI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.153 (Depositor), 0.161 (DCC)
R-Value Work:
0.133 (Depositor), 0.142 (DCC)
R-Value Observed:
0.134 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii .

Favretto, F., Jimenez-Faraco, E., Conter, C., Dominici, P., Hermoso, J.A., Astegno, A.

(2023) ACS Infect Dis 9: 365-377

PubMed: 36653744 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsinfecdis.2c00566
Primary Citation Related Structures:
8B58

PubMed Abstract:
Cyclosporin (CsA) has antiparasite activity against the human pathogen Toxoplasma gondii . A possible mechanism of action involves CsA binding to T. gondii cyclophilins, although much remains to be understood. Herein, we characterize the functional and structural properties of a conserved (TgCyp23) and a more divergent (TgCyp18.4) cyclophilin isoform from T. gondii . While TgCyp23 is a highly active cis-trans-prolyl isomerase (PPIase) and binds CsA with nanomolar affinity, TgCyp18.4 shows low PPIase activity and is significantly less sensitive to CsA inhibition. The crystal structure of the TgCyp23:CsA complex was solved at the atomic resolution showing the molecular details of CsA recognition by the protein. Computational and structural studies revealed relevant differences at the CsA-binding site between TgCyp18.4 and TgCyp23, suggesting that the two cyclophilins might have distinct functions in the parasite. These studies highlight the extensive diversification of TgCyps and pave the way for antiparasite interventions based on selective targeting of cyclophilins.

Organizational Affiliation

Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy.

Macromolecule Content

Total Structure Weight: 48.44 kDa
Atom Count: 3,824
Modeled Residue Count: 421
Deposited Residue Count: 444
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A, B	211	Toxoplasma gondii	Mutation(s): 0 Gene Names: TGRH88_026260 EC: 5.2.1.8
UniProt
Find proteins for B9PS61 (Toxoplasma gondii (strain ATCC 50861 / VEG)) Explore B9PS61 Go to UniProtKB: B9PS61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9PS61
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclosporin A	C, D	11	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	C, D	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	C, D	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	C, D	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142 Query on PRD_000142	C, D	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.153 (Depositor), 0.161 (DCC)
R-Value Work: 0.133 (Depositor), 0.142 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.4	α = 90
b = 119.424	β = 103.62
c = 46.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Jimenez-Faraco, E.

Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	PID2020-115331GB-I00

Revision History (Full details and data files)

Version 1.0: 2023-02-01
Type: Initial release
Version 1.1: 2023-02-22
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.