Structure of the β2 homodimer of bacterial luciferase from vibrio harveyi: X‐ray analysis of a kinetic protein folding trap

Open Access
Publisher Website
Google Scholar
Abstract
Luciferase, as isolated from Vibrio harveyi, is an aβ heterodimer. When allowed to fold in the absence of the α subunit, either in vitro or in vivo, the β subunit of the enzyme will form a kinetically stable homodimer that does not unfold even after prolonged incubation in 5 M urea at pH 7.0 and 18 °C. This form of the β subunit, arising via kinetic partitioning on the folding pathway, appears to constitute a kinetically trapped alternative to the heterodimeric enzyme (Sinclair JF, Ziegler MM, Baldwin TO. 1994. Kinetic partitioning during protein folding yields multiple native states. Nature Struct Biol 1: 320–326). Here we describe the X‐ray crystal structure of the β2 homodimer of luciferase from V. harveyi determined and refined at 1.95 Å resolution. Crystals employed in the investigation belonged to the orthorhombic space group P212121 with unit cell dimensions of a = 58.8 Å, b = 62.0 Å, and c = 218.2 Å and contained one dimer per asymmetric unit. Like that observed in the functional luciferase αβ heterodimer, the major tertiary structural motif of each β subunit consists of an (α/β)8 barrel (Fisher AJ, Raushel FM, Baldwin TO, Rayment I. 1995. Three‐dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 Å resolution. Biochemistry 34: 6581–6586). The root‐mean‐square deviation of the α‐carbon coordinates between the β subunits of the hetero‐ and homodimers is 0.7 Å. This high resolution X‐ray analysis demonstrates that “domain” or “loop” swapping has not occurred upon formation of the β2 homodimer and thus the stability of the β2 species to denaturation cannot be explained in such simple terms. In fact, the subunit:subunit interfaces observed in both the β2 homodimer and αβ heterodimer are remarkably similar in hydrogen‐bonding patterns and buried surface areas.
Funding Information
  • NIH (AR35186 and DK47814)
  • NSF (BIR-9317398)
  • Office of Naval Research (N00014-96-1-0087 and N00014-93-1-1345)
  • Robert A. Welch Foundation ((A-865 to T.O.B.))
  • NSRA fellowships (AR08304 and GM15950)