Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Sep 15;48(36):8664-71.
doi: 10.1021/bi900437z.

Structure and Function of Bacillus Subtilis YphP, a Prokaryotic Disulfide Isomerase With a CXC Catalytic Motif

Affiliations
Free PMC article

Structure and Function of Bacillus Subtilis YphP, a Prokaryotic Disulfide Isomerase With a CXC Catalytic Motif

Urszula Derewenda et al. Biochemistry. .
Free PMC article

Abstract

The DUF1094 family contains over 100 bacterial proteins, all containing a conserved CXC motif, with unknown function. We solved the crystal structure of the Bacillus subtilis representative, the product of the yphP gene. The protein shows remarkable structural similarity to thioredoxins, with a canonical alphabetaalphabetaalphabetabetaalpha topology, despite low amino acid sequence identity to thioredoxin. The CXC motif is found in the loop immediately downstream of the first beta-strand, in a location equivalent to the CXXC motif of thioredoxins, with the first Cys occupying a position equivalent to the first Cys in canonical thioredoxin. The experimentally determined reduction potential of YphP is E degrees' = -130 mV, significantly higher than that of thioredoxin and consistent with disulfide isomerase activity. Functional assays confirmed that the protein displays a level of isomerase activity that might be biologically significant. We propose a mechanism by which the members of this family catalyze isomerization using the CXC catalytic site.

Figures

Figure 1
Figure 1
(A) Packing of four crystallographically independent molecules of YphP. (B) A single molecule of YphP with the secondary structure elements identified (α-helices red and β-strands yellow) and the two Cys side chains of the CXC motif shown as spheres and labeled; the additional N-terminal α-helix unique to the DUF1094 family is shown in cyan. (C) Analogous view of the human thioredoxin (PDB code 1AUC) shown for comparison. The annotations used here for the α-helices and β-sheets follow the standard convention for thioredoxins (45).
Figure 2
Figure 2
Structure of the catalytic loop of YphP. The coordinates used in this diagram are those of chain D but are representative of all four chains in the structure.
Figure 3
Figure 3
Sequence alignment of representative members of the DUF1094 family. Black triangles show the four residues that we identify as the catalytic amino acids (further details in the text). Semiconserved and fully conserved residues are indicated by darkening blue color. The secondary structure elements are shown below the alignment as cylinders (α-helices) and arrows (β-sheets).
Figure 4
Figure 4
Reduction potential of YphP. The fraction of reduced YphP (f) is plotted as a function of the solution reduction potential, which was established at 30 °C by using reduced and oxidized glutathione. Values are the mean (±SE) from three experiments. The data were fitted to eq 2 to give E°′ = −130 ± 5 mV.
Figure 5
Figure 5
Diagram of the proposed reaction mechanism catalyzed by YphP and its homologues.
Figure 6
Figure 6
Structures of known oxidized CXC motifs and the reduced CXC motif of YphP; for details see text. The colors reflect atom type: yellow, carbon; blue, nitrogen; red, oxygen; green, sulfur.

Similar articles

See all similar articles

Cited by 17 articles

See all "Cited by" articles

References

    1. Ginalski K.; Elofsson A.; Fischer D.; Rychlewski L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19, 1015–1018. - PubMed
    1. von Grotthuss M.; Pas J.; Wyrwicz L.; Ginalski K.; Rychlewski L. (2003) Application of 3D-Jury, GRDB, and Verify3D in fold recognition. Proteins 53, Suppl. 6418–423. - PubMed
    1. Pan J. L.; Bardwell J. C. (2006) The origami of thioredoxin-like folds. Protein Sci. 15, 2217–2227. - PMC - PubMed
    1. Quan S.; Schneider I.; Pan J.; Von Hacht A.; Bardwell J. C. (2007) The CXXC motif is more than a redox rheostat. J. Biol. Chem. 282, 28823–28833. - PubMed
    1. Grauschopf U.; Winther J. R.; Korber P.; Zander T.; Dallinger P.; Bardwell J. C. (1995) Why is DsbA such an oxidizing disulfide catalyst?. Cell 83, 947–955. - PubMed

Publication types

MeSH terms

Associated data

LinkOut - more resources

Feedback