PDBsum entry 2c3b

Isomerase

PDB id: 2c3b

Contents

Protein chains

141 a.a. *

Ligands

SO4 ×2

Waters ×123

* Residue conservation analysis

PDB id:

2c3b

Name:

Isomerase

Title:

The crystal structure of aspergillus fumigatus cyclophilin reveals 3d domain swapping of a central element

Structure:

Ppiase. Chain: a, b. Synonym: cyclophilin. Engineered: yes

Source:

Aspergillus fumigatus. Organism_taxid: 5085. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.85Å R-factor: 0.191 R-free: 0.214

Authors:

A.Limacher,D.P.Kloer,S.Fluckiger,G.Folkers,R.Crameri,L.Scapozza

Key ref:

A.Limacher et al. (2006). The Crystal Structure of Aspergillus fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element. Structure, 14, 185-195. PubMed id: 16472738 DOI: 10.1016/j.str.2005.10.015

Date:

05-Oct-05 Release date: 30-Jan-06

Protein chains

Q4WHY9  (Q4WHY9_ASPFU) -  Peptidyl-prolyl cis-trans isomerase from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)

Seq: 205 a.a.

Struc: 141 a.a.

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: 10.1016/j.str.2005.10.015

Structure 14:185-195 (2006)

PubMed id: 16472738

The Crystal Structure of Aspergillus fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element.

A.Limacher, D.P.Kloer, S.Flückiger, G.Folkers, R.Crameri, L.Scapozza.

ABSTRACT

The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

Selected figure(s)

Figure 3.
Figure 3. W Loop Bound to Active Site and Second Hinge Loop
(A) Electron density of the second hinge loop and parts of the adjacent W loop (aa 124-129). The experimental map is contoured at 1s using solvent-flattened experimental phases calculated without NCS averaging. H bonds within and between the hinges of both chains are indicated by yellow, dashed lines. Residues of chain A and B are colored in violet and green, respectively.
(B) Hydrophobic binding of the W loop into its own active site. Trp124 and Leu125 of chain A sit into the hydrophobic pocket of subunit A, making hydrophobic interactions with surrounding residues of both chains. In subunit B, Val121 and Trp124 of chain B sit into its active site. Position and conformation of some distinctive residues of human CyPA (2CPL) are shown for comparison. Two independent monomers of CyPA were superimposed on either subunit of Asp f 11 (see Figure 1C). Side chains of CyPA superposed on subunit A and B are colored in orange and yellow, respectively.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 185-195) copyright 2006.

Figure was selected by an automated process.