Modelling of steric structure of a periplasmic molecular chaperone Caf1M ofYersinia pestis, a prototype member of a subfamily with characteristic structural and functional features

Abstract

Steric structure of Caf1M, a periplasmic molecular chaperone of Yersinia pestis, was reconstructed by computer modelling based on a statistically significant primary structure homology between Caf1M and PapD protein from Escherichia coli, and using the known atomic coordinates obtained by the X-ray crystallography for PapD. In the three-dimensional model of Caf1M an accessory sequence between F1 and G1 beta-strands (as compared to PapD) can form a strain-specific part of the binding pocket of surface organell subunits. This accessory sequence decreases the depth of the binding pocket. The characteristic structural feature of the subfamily of periplasmic molecular chaperones with the accessory sequence (Caf1M subfamily) is the existence of exposed to a solvent Cys residues in F1 and G1 beta-strands which can form disulfide bond in the putative binding pocket. The characteristic functional feature of Caf1M subfamily is the chaperoning of more simple compositions of virulence-associated surface organells (in the case of Y. pestis a capsule consists of only F1 protein). Highly conserved R82 and D93, located at the domain surface remote from the putative subunit binding pocket, can participate in direct contacts with the conserved portion of molecular usher proteins.

Influence of the conserved disulphide bond, exposed to the putative binding pocket, on the structure and function of the immunoglobulin-like molecular chaperone Caf1M of Yersinia pestis

“…The CD spectra reveal a high content of β-structure and a very low content of α-helix for all proteins analysed (Table 1), in accordance with the X-ray analysis data for immunoglobulins [21], with the PapD-like model of the threedimensional structure of Caf1M [10], and with the predicted immunoglobulin-like fold of small heat-shock proteins [22]. However, there are some significant differences.…”

“…The periplasmic molecular chaperone Caf1M of Y. pestis contains two cysteine residues per molecule [5], positioned at a distance that would permit formation of a disulphide bond [10]. As free SH groups of cysteine residues, in contrast with disulphide bonds, interact specifically with maleimide conjugates [17], we used blotting with biotin-maleimide to monitor for the presence of free SH groups in the Caf1M molecule.…”

“…Based on this assumption, the steric structure of the Y. pestis chaperone Caf1M was reconstructed by computer modelling using the atomic co-ordinates for PapD [10]. In our previous analysis of the primary structure alignment of 17 of the periplasmic chaperones, we discovered that Caf1M belongs to a subfamily of seven chaperones [10].…”

“…In our previous analysis of the primary structure alignment of 17 of the periplasmic chaperones, we discovered that Caf1M belongs to a subfamily of seven chaperones [10]. This subfamily is characterized by possession of (i) two cysteine residues, one located in the F1 β-strand and the other in the G1 β-strand, with the potential of forming a disulphide bond exposed to the putative subunit binding pocket, and (ii) an accessory sequence encompassed by the two cysteine residues [10]. We also noted that a characteristic functional feature of the Caf1M-like subfamily is the chaperoning of virulence-associated surface organelles with a simple composition; for example, the Y. pestis capsule consists of a single subunit, Caf1.…”

“…Based on this assumption, the steric structure of the Y. pestis chaperone Caf1M was reconstructed by computer modelling using the atomic co-ordinates for PapD [10]. In our previous analysis of the primary structure alignment of 17 of the periplasmic chaperones, we discovered that Caf1M belongs to a subfamily of seven chaperones [10]. This subfamily is characterized by possession of (i) two cysteine residues, one located in the F1 β-strand and the other in the G1 β-strand, with the potential of forming a disulphide bond exposed to the putative subunit binding pocket, and (ii) an accessory sequence encompassed by the two cysteine residues [10].…”