1ZKC

Crystal Structure of the cyclophiln_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2 isoform b

PDB DOI: 10.2210/pdb1ZKC/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-05-02 Released: 2005-08-16
Deposition Author(s): Walker, J.R., Davis, T., Newman, E.M., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.194
R-Value Work: 0.156
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.

Davis, T.L., Walker, J.R., Campagna-Slater, V., Finerty, P.J., Paramanathan, R., Bernstein, G., MacKenzie, F., Tempel, W., Ouyang, H., Lee, W.H., Eisenmesser, E.Z., Dhe-Paganon, S.

(2010) PLoS Biol 8: e1000439-e1000439

PubMed: 20676357 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pbio.1000439
Primary Citation of Related Structures:
1ZKC, 2ESL, 2GW2, 2HE9, 2HQ6, 2R99

PubMed Abstract:

Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure:function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity.

Organizational Affiliation:

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase like 2	A, B	197	Homo sapiens	Mutation(s): 0 Gene Names: PPIL2 EC: 5.2.1.8 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13356 (Homo sapiens) Explore Q13356 Go to UniProtKB: Q13356
PHAROS: Q13356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13356
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Ligand Interaction