He predicted ORF encodes a 71-aa protein bearing 31 identity and 53 similarity

He predicted ORF encodes a 71-aa protein bearing 31 identity and 53 similarity to RsmA (Fig. 1A). Given the restricted homology with the putative gene solution with CsrA, RsmA, and RsmE, the gene was designated rsmF. All previously characterized CsrA proteins possess a very conserved secondary structure consisting of 5 -strands and also a carboxyl-terminal (C-terminal) -helix (4, 13, 16, 17). Analysis of your predicted RsmF sequence revealed a unique insertion amongst -strands two and three, as well as a C-terminal deletion relative to other CsrA family members (Fig. 1A).Author contributions: J.N.M., M.R.D., C.J.G., M.L.U., T.L.Y., and M.C.W. made investigation; J.N.M., M.R.D., W.G.W., C.J.G., L.B., M.L.U., T.L.Y., and M.C.W. performed investigation; J.N.M., M.R.D., C.J.G., M.L.U., T.L.Y., and M.C.W. contributed new reagents/ analytic tools; J.N.M., M.R.D., W.G.W., C.J.G., L.B., M.L.U., M.R.R., T.L.Y., and M.C.W. analyzed information; and J.N.M., M.R.D., C.J.G., M.R.R., T.L.Y., and M.C.W. wrote the paper. The authors declare no conflict of interest. This article is usually a PNAS Direct Submission. Data deposition: The RsmF coordinates and structure factors happen to be deposited in the Protein Data Bank, www.pdb.org (PDB ID code 4K59). The RsmF key sequence has been deposited within the GenBank database [accession no. KF364633 (strain PA103)].1J.N.M. and M.R.D. contributed equally to this perform. To whom correspondence needs to be addressed.Tegoprubart E-mail: matthew_wolfgang@med.Avexitide unc. edu.This short article includes supporting details on-line at www.pnas.org/lookup/suppl/doi:10. 1073/pnas.1307217110/-/DCSupplemental.PNAS | September 10, 2013 | vol. 110 | no. 37 | 15055MICROBIOLOGYAB13C53341 four 44Fig. 1. RsmF structure. (A) Major sequence alignment of E. coli (Ec) CsrA, P. aeruginosa (Pa) RsmA and RsmF, and P. fluorescens (Pf) RsmA and RsmE. All 5 proteins consist of five -strands (1) and one major -helix (1), but the organization of these components is distinct for RsmF. Conserved arginine residues essential for maximal CsrA/RsmA RNA-binding activity are boxed. (B and C) Ribbon diagrams on the RsmF crystal structure as a homodimer (B) plus the reported option structure of P. fluorescens dimeric RsmE (pdb ID 2JPP), a homolog of P. aeruginosa RsmA (C).To identify irrespective of whether RsmF maintained the all round architecture of other CsrA proteins, we determined the crystal structure at 2.2-resolution and refined it to R and Rfree values of 0.21 and 0.27, respectively (SI Appendix, Table S1). RsmF types a dimer, with residues 15 of each monomer ordered in the final structure (Fig.PMID:23880095 1B). The RsmF dimer is developed by two antiparallel -sheets, each composed of 1, 3, and four from 1 protein monomer, and 2 and five from the other (SI Appendix, Fig. S2A). The -helices of every single RsmF monomer, positioned amongst -strands 2 and three, interact with each other and are located above the central area of the dimer (Figs. 1B and SI Appendix, S2A). This arrangement differs from CsrA members of the family of known structure in that the antiparallel -sheets are composed of 1 and 5 from a single monomer and 2, three, and 4 in the other monomer (Fig. 1C and SI Appendix, Fig. S2B) (4, 13, 16, 17). Moreover, the C-terminal -helices of typical CsrA/RsmA monomers usually do not interact and are arranged as wings extending from the sides of your dimer (Fig. 1C). Despite the topological variations and positioning of the -helices, the structure in the RsmF -sandwich is largely comparable to other CsrA proteins, suggesting that it might possess an analogous regulatory.