Figure 4

Subunit assembly and surface structure of NylC. (a) Model of the subunit assembly of NylC. The oligomeric states are dynamically altered depending on the structural changes caused by mutations. Typical association/dissociation reactions (reactions 1–8) are shown. Major assembly and dissociation reactions are assumed to be in equilibrium and are shown as solid lines (reactions 1 and 2), while the alternative equilibria shown as dashed lines may be possible. To simplify the designation of each monomer molecule in the quaternary structure, both the uncleaved precursor and the cleaved enzyme (αβ heterodimer) are expressed as molecules A-D. (b) Monomer (A), dimer (A/B and A/D), trimer (A/B/C), and tetramer structures are shown as surface models. Contacts at the A/B and C/D interfaces (3,121 Ų) were observed to be more extensive than those at the B/C and A/D interfaces (1,451 Ų). (c) The tetramer structure of the NylC_p2-G¹²²Y¹³⁰A³⁶Q²⁶³ mutant is shown as a space-filling model. The overall structures of monomer molecules A, B, C, and D are shown in light green, light blue, light pink, and light yellow, respectively. To highlight the catalytic residues and mutated sites, the catalytic nucleophile Thr267 (in the N-terminus of the β subunit in monomer A) and other presumed catalytic residues (Lys189 and Asn219) are shown in red, dark blue, and dark green, respectively. The mutated residues (Ala36, Gly122, Tyr130, and Leu137) in monomer A are shown in purple. The mutated residues (Ala36, Tyr130, and Leu137) in monomer D are shown in orange. The conformation of the Glu263 side chain in NylC_p2-G¹²²Y¹³⁰A³⁶Q²⁶³ could not be determined due to poor electron density. Pro259/Pro260, which is linked to the loop 5 region, is shown in green (monomer A) and magenta (monomer C). Arg328 and Arg330 in loop 7 are marked. (d) To show the structure of the A/D interface in the NylC_p2-G¹²²Y¹³⁰A³⁶Q²⁶³ mutant, the structure (space-filling model) is shown by omitting monomer D.