X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family

Abstract

Background: Pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs).

Results: Crystal structures of two proteins from Deinococcus radiodurans and Streptomyces coelicolor belonging to Pfam protein family DUF178 (ID: PF02621) have been determined using Selenium-Single-wavelength Anomalous Dispersion (Se-SAD). Based on the structure, we have identified the putative function for this family of protein.

Conclusion: Unexpectedly, we found that DUF178 Pfam is remarkably similar to Pfam family DUF191 suggesting that the sequence-based classification alone may not be sufficient to classify proteins into Pfam families.

Figure 1

Multiple sequence alignment of DUF178 from various organisms. The residues highlighted in orange are the conserved residues (*). The abbreviations for organism names are as follows: Dra; Deinococcus radiodurans (10093b), Fsp; Frankia sp. CcI3, Sco; Streptomyces coelicolor (10093f), Dre; Desulfotomaculum reducens, Sth; Symbiobacterium thermophilum, Gme; Geobacter metallireducens, Tth; Thermus thermophilus, Cks; Candidatus Kuenenia stuttgarti, Cab; Chlamydophila abortus. The secondary structural elements for 10093b (residues 16 to 285) are given at the top of alignment.

Figure 2

(A) Monomer of 10093b showing both N- & C-terminal domains. The 10093f monomer has the same fold. (B) Asymmetric unit of 10093b showing tightly packed dimer. Loop responsible for dimerization is labeled.

Figure 3

Stereoviews of (A) superposition of 10093b (red) and 10093f (green) monomers. The loop exclusive to 10093b is labeled. (B) superposition of 10093b (green) and 10093f (magenta) dimer. While 10093b is a dimer in solution, the dimerization of 10093f is due to crystal packing effect. (C) superposition of 10093b (red) and 1ZBM (blue) monomers.

Figure 4

Zoom view showing putative binding site of 10093b. The β-strands (yellow ribbon), α-helices (red ribbon), and random coil (green ribbon), plus clustered conserved residues Asn26, Pro47, Ser92, Ser113, Ser116, Ile154, Gly155, and Asp156 from multiple sequence alignment shown in figure 1 (atom color coded stick figures; N-blue; C-sky blue; O-red). All residues numbers are labelled in black.