Abstract
Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions used for structure determination using NMR spectroscopy. The structure of the Dsy0195 homodimer contains two identical 62-residue monomeric subunits, each consisting of five anti-parallel beta strands (β1, 23–29; β2, 31–38; β3, 41–46; β4, 49–59; β5, 69–80). The tertiary structure of the Dsy0195 monomer adopts a cylindrical fold composed of two beta sheets. The two monomer subunits fold into a homodimer about a single C2 symmetry axis, with the interface composed of two anti-parallel beta strands, β1–β1′ and β5b–β5b′, where β5b refers to the C-terminal half of the bent β5 strand, without any domain swapping. Potential functional regions of the Dsy0195 structure were predicted based on conserved sequence analysis. The Dsy0195 structure reported here is the first representative structure from the YabP family.
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Abbreviations
- DEER:
-
Double electron electron resonance
- GFP:
-
Green flourescent protein
- MTSL:
-
(1-Oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate
- NESG:
-
Northeast structural genomics consortium
- NMR:
-
Nuclear magnetic resonance spectroscopy
- NOE:
-
Nuclear overhauser effect
- NOESY:
-
Nuclear overhauser effect spectroscopy
- PRE:
-
Paramagnetic relaxation enhancement
- RMSD:
-
Root mean square deviation
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Acknowledgments
This work was supported by the National Institute of General Medical Sciences; Grant Number: U54-GM074958. The majority of the data collection was conducted at the Ohio Biomedicine Center of Excellence in Structural Biology and Metabonomics at Miami University. A portion of the NMR experiments was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the US Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.
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Yang, Y., Ramelot, T.A., Cort, J.R. et al. Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly. J Struct Funct Genomics 12, 175–179 (2011). https://doi.org/10.1007/s10969-011-9117-z
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DOI: https://doi.org/10.1007/s10969-011-9117-z