Similarities and differences between human cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 A resolution.

The structure of the unligated recombinant human cyclophilin A (CyP A) has been refined to an R-factor of 0.18 at 1.63 A resolution. The root-mean-squared deviations of the refined structure are 0.013 A and 2.50 degrees from ideal geometries of bond length and bond angle, respectively. Eight antiparallel beta-strands of CyP A form a right-handed beta-barrel. The structure of CyP A is compared with other members in the antiparallel eight-stranded beta-barrel family and with the parallel eight-stranded alpha/beta barrels. Although all known eight-stranded barrels are right-handed, the tilted angle of the strands against the barrel axis varies from 45 degrees for retinol binding protein and 49 degrees for CyP A to 70 degrees for superoxide dismutase. As a result, the beta-barrel of CyP A is not completely superimposable with other members of beta-barrels. The structure of CyP A has a unique topology, distinct from other members in the beta-barrel family. In addition, CyP A is a closed beta-barrel so that neither the immunosuppressive drug cyclosporin A (CsA) nor the proline-containing substrate can bind to the hydrophobic core of the CyP A barrel, while the hydrophobic core of most other barrels is open for ligation. These observations probably indicate that CyP A is neither functionally nor evolutionally related to other beta-barrel structures. Details of interactions between solvent molecules and the active site residues of CyP A are illustrated. A water-co-operated mechanism, where the cis<-->trans isomerization might possibly consist of (1) transition of the prolyl bond and (2) release of N or C-terminal residues of substrate from CyP, is addressed. The refined structure reveals no disulfide bridges in CyP A. Cys115 is near the CsA site, but unlikely to be directly involved in CsA binding because of steric hindrance from Thr119 and Leu122. This geometry probably rules out any mechanisms involving a tetrahedral intermediate formed between cysteine and substrate during cis<-->trans isomerization.

[1]  W. Bode,et al.  The refined crystal structure of bovine β-trypsin at 1·8 Å resolution , 1975 .

[2]  B. Haendler,et al.  A novel secreted cyclophilin-like protein (SCYLP). , 1991, The Journal of biological chemistry.

[3]  W. Bode,et al.  The refined crystal structure of bovine beta-trypsin at 1.8 A resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0. , 1975, Journal of molecular biology.

[4]  Stephen W. Fesik,et al.  A model of the cyclophilin/cyclosporin A (CSA) complex from NMR and X-ray data suggests that CSA binds as a transition-state analog , 1992 .

[5]  D. Speicher,et al.  Cyclophilin: a specific cytosolic binding protein for cyclosporin A. , 1984, Science.

[6]  M. Harding,et al.  Cyclophilin: distribution and variant properties in normal and neoplastic tissues. , 1986, Journal of immunology.

[7]  T A Jones,et al.  The three‐dimensional structure of P2 myelin protein. , 1988, The EMBO journal.

[8]  Short-range flaws , 1992, Nature.

[9]  L. Sawyer.  One fold among many , 1987, Nature.

[10]  C. Walsh,et al.  Human cyclophilin B: a second cyclophilin gene encodes a peptidyl-prolyl isomerase with a signal sequence. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Friedman,et al.  Two cytoplasmic candidates for immunophilin action are revealed by affinity for a new cyclophilin: One in the presence and one in the absence of CsA , 1991, Cell.

[12]  J. L. Smith,et al.  Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[13]  W. Lipscomb,et al.  Structure refinement of fructose-1,6-bisphosphatase and its fructose 2,6-bisphosphate complex at 2.8 A resolution. , 1990, Journal of molecular biology.

[14]  P. Kraulis,et al.  The structure of β-lactoglobulin and its similarity to plasma retinol-binding protein , 1986, Nature.

[15]  I. Rayment,et al.  The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution. , 1987, The EMBO journal.

[16]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[17]  G. Wider,et al.  Structure of human cyclophilin and its binding site for cyclosporin A determined by X-ray crystallography and NMR spectroscopy , 1991, Nature.

[18]  P. A. Peterson,et al.  The three‐dimensional structure of retinol‐binding protein. , 1984, The EMBO journal.

[19]  J. Richardson,et al.  Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. , 1980, Journal of molecular biology.

[20]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[21]  T. Hayano,et al.  Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin , 1989, Nature.

[22]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[23]  F. Schmid,et al.  The mechanism of protein folding. Implications of in vitro refolding models for de novo protein folding and translocation in the cell. , 1990, Biochemistry.

[24]  R. Stein,et al.  Mechanistic studies of peptidyl prolyl cis-trans isomerase: evidence for catalysis by distortion. , 1990, Biochemistry.

[25]  Kuo-Chen Chou,et al.  Conformational and geometrical properties of idealized β-barrels in proteins , 1990 .

[26]  Jun O. Liu,et al.  Cloning, expression, and purification of human cyclophilin in Escherichia coli and assessment of the catalytic role of cysteines by site-directed mutagenesis. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[27]  K. Wüthrich,et al.  Nmr studies of the rates of proline cis–trans isomerization in oligopeptides , 1981 .

[28]  G. Fischer,et al.  Kinetic β‐deuterium isotope effects suggest a covalent mechanism for the protein folding enzyme peptidylprolyl cis/trans‐isomerase , 1989, FEBS letters.

[29]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[30]  C. Chothia,et al.  Orthogonal packing of beta-pleated sheets in proteins. , 1982, Biochemistry.

[31]  R. Huber,et al.  Crystallization, crystal structure analysis and preliminary molecular model of the bilin binding protein from the insect Pieris brassicae. , 1987, Journal of molecular biology.

[32]  T. Kiefhaber,et al.  Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins , 1989, Nature.

[33]  Stuart L. Schreiber,et al.  Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes , 1991, Cell.