PDBsum entry 2bit

Isomerase

PDB id: 2bit

Contents

Protein chain

164 a.a. *

Waters ×393

* Residue conservation analysis

PDB id:

2bit

Name:

Isomerase

Title:

Crystal structure of human cyclophilin d at 1.7 a resolution

Structure:

Peptidyl-prolyl cis-trans isomerase. Chain: x. Fragment: residues 43-207. Synonym: cyclophilin f, ppiase, rotamase, cyclophilin d. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.71Å R-factor: 0.141 R-free: 0.175

Authors:

M.Hennig,R.Thoma,M.Stihle,D.Schlatter

Key ref:

D.Schlatter et al. (2005). Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution. Acta Crystallogr D Biol Crystallogr, 61, 513-519. PubMed id: 15858260 DOI: 10.1107/S0907444905003070

Date:

26-Jan-05 Release date: 26-Jan-05

Protein chain

P30405  (PPIF_HUMAN) -  Peptidyl-prolyl cis-trans isomerase F, mitochondrial from Homo sapiens

Seq: 207 a.a.

Struc: 164 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1107/S0907444905003070

Acta Crystallogr D Biol Crystallogr 61:513-519 (2005)

PubMed id: 15858260

Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution.

D.Schlatter, R.Thoma, E.Küng, M.Stihle, F.Müller, E.Borroni, A.Cesura, M.Hennig.

ABSTRACT

In the pharmaceutical industry, knowledge of the three-dimensional structure of a specific target facilitates the drug-discovery process. Despite possessing favoured analytical properties such as high purity and monodispersion in light scattering, some proteins are not capable of forming crystals suitable for X-ray analysis. Cyclophilin D, an isoform of cyclophilin that is expressed in the mitochondria, was selected as a drug target for the treatment of cardiac disorders. As the wild-type enzyme defied all attempts at crystallization, protein engineering on the enzyme surface was performed. The K133I mutant gave crystals that diffracted to 1.7 A resolution using in-house X-ray facilities and were suitable for soaking experiments. The crystals were very robust and diffraction was maintained after soaking in 25% DMSO solution: excellent conditions for the rapid analysis of complex structures including crystallographic fragment screening.

Selected figure(s)

Figure 5.
Figure 5 (a) Stereoview in ball-and-stick representation with sticks coloured blue and yellow for the molecules that form the crystal contact. The mutation K133I favors the formation of the crystal contact with mainly hydrophobic interactions. A lysine side chain at this position would cause steric clashes and disable this crystal packing.

Figure 6.
Figure 6 Soaking with 25% DMSO resulted in four DMSO-binding sites with very high confidence. Two DMSO molecules were identified in close proximity to the active site of the enzyme. DMSO-1 forms a hydrogen bond to the guanidine group of Arg55 and DMSO-2 forms a hydrogen bond to Asn102 NH, a hydrogen bond that is also formed in the complex of cyclophilin A with cyclosporin A.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 513-519) copyright 2005.

Figures were selected by an automated process.