PMC:7094172 / 4762-10117 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7094172","sourcedb":"PMC","sourceid":"7094172","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7094172","text":"Structure of the N-Terminal Domain of the MERS-CoV N Protein\nWe determined the crystal structure of MERS-CoV N-NTD by molecular replacement (MR) using the structure of HCoV-OC43 N-NTD (PDB ID: 4J3K) as the search model.24 The final structure was refined to R-factor and R-free values of 0.26 and 0.29, respectively, at a resolution of 2.6 Å (Table S1). Each asymmetric unit contained four N-NTD molecules assembled into two identical dimers with an overall RMSD of 0.28 Å between the dimers (Figure S1A,B). The monomers shared a similar structural core preceded by a flexible region (Figure S1D). The core consisted of a five-stranded antiparallel β-sheet sandwiched between loops arranged in a right-handed, fist-shaped structure conserved among the CoVs.25 In our structure, however, the loop connecting strands β2 and β3 protruding out of the core into other CoV N proteins was absent. Unlike the reported structures that have a monomeric conformation, our structure was atypically dimeric.\nFigure 1B shows the details of the interactions in the MERS-CoV N protein dimer. We named the units monomer 1 and monomer 2 (Figure 1A). According to the amino acid composition of the binding site on monomer 2, we divided the dimeric interface into two areas: one located on the N-terminus flexible region and the other on the loop between β4 and β5 of the N protein. In the first area, W43, N66, N68, Y102, and F135 of monomer 1 generated a conserved hydrophobic pocket permitting the side chain of M38 of monomer 2 to enter this hole by a hydrophobic contact (Figure 1C,D). H37 and N39 of monomer 2 were packed against W43 and F135 of monomer 1, respectively, and contributed to the hydrophobic interaction. The side chains of N39 of monomer 2 formed one hydrogen bond with the N68 backbone in monomer 1 at a distance of 2.6 Å. The second area was relatively more hydrophilic. The main chain oxygens of G104, F135, and T137 of monomer 2 formed three hydrogen bonds with the side chains of Q73 and T134 of monomer 1 at distances of 3.8, 3.2, and 3.7 Å, respectively. The side chain of N139 on monomer 2 formed a hydrogen bond with the main chain oxygen of T137 on monomer 1 at a distance of 3.6 Å. The interactions of the first and second areas comprise buried surface areas (BSA) of 289 and 103 Å2, respectively. The small surface area buried at the interface accounts for ∼5 kcal mol–1 binding energy,26 which translates to a dissociation constant of ∼200 mM. Thus, the dimer described here is unique in that it is non-native and relies on vector-fusion residues (H37 and M38) to maintain its dimeric status. This property may also explain why the present structure has an oligomeric status different from previously reported structures for the CoV N protein.24,27−30 We used cross-linking experiments to analyze the oligomeric capacity of MERS N-NTD containing the vector-fusion residues in solution. MERS N-NTD had a dimeric conformation in solution. Our structure indicated that W43 played an essential role in forming the hydrophobic pocket accommodating the vector-fusion residues and, therefore, mediated the N-NTD dimer formation. The W43A mutation significantly reduced the oligomeric tendency of N-NTD (Figure S1C). This further supports that the “exogenous residues” encoded by the vector backbone mediated the formation of the non-native dimer. We also superimposed the previously published structure of MERS-CoV N-NTD (PDB ID: 4ud1)27 containing a native N-terminal flexible region with our dimer structure. The side chain of N38 in the native structure could not interact with the hydrophobic pocket as the former is hydrophilic and short (Figure S1E). Thus, it may be possible to utilize small compounds to replace the vector-fusion residues and stabilize the PPI through hydrophobic interactions.\nFigure 1 Structure and sequence of MERS-CoV N-NTD. (A) Overall structure of the MERS-CoV N-NTD dimer containing monomers 1 and 2 is depicted as a cartoon and colored yellow and green, respectively. Residues involved in dimerization are shown as sticks and highlighted in (B). (B) Interactions among MERS-CoV N-NTDs. Dimerization is mediated mainly by vector-fusion residues interacting with the conserved hydrophobic regions on the core structure (first area) along with the residues surrounding it (second area). Interacting residues on monomers 1 and 2 are labeled in black and blue, respectively. Vector-fusion and conserved hydrophobic regions are colored cyan and red, respectively. The color of all other interacting residues is the same as that for each monomer in (A). Polar contacts are indicated with red dashed lines. (C) Upper panel: close-up of the interacting region of vector-fusion residues. The surface was colored according to the hydrophobicity level at the protein surface. Vector-fusion residues (black) are shown as sticks to emphasize the hydrophobic pocket. Lower panel: 2D diagrams of the interaction between the hydrophobic pocket and the vector-fusion residues. The latter are labeled in black. The hydrophobic contacts are indicated with black dashed lines. (D) Sequence alignment of various CoV N proteins in the N-terminal region. Red letters indicate strictly conserved residues. Cyan indicates conservative substitution sites. Hydrophobic regions involved in unusual dimerization are indicated by black 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