Determination of the solution structure of the N-domain plus linker of antarctic eel pout antifreeze protein RD3

RD3, a new antifreeze protein (AFP) extracted from antarctic eel pout is a single polypeptide divided into homologous N-terminal (residues Asn(1)-Glu(64)) and C-terminal (residues Ser(74)-Glu(134)) domains, each of which has a high sequence identity with Type III AFP, A 9-residue linker (-D(65)GTTSPGLK(73)-) connects these two domains in tandem and is thought to play a significant role in defining the nature of the intact molecule. The present paper shows for the first time the solution structure and preliminary N-15-NMR backbone dynamics data of the N-domain plus the linker of recombinant RD3 protein (RD3-N1: residues 1-73) by employing homo- and heteronuclear multidimensional NMR spectroscopy. Forty converged structures of RD3-NI were successfully calculated by using a total of 958 NMR-derived structural restraints, It was found that the N-domain of RD3-N1 has a globular form comprising six beta-strands, three type III turns, and several loops, which stabilize a flat, ice-binding site formed on one side of this domain. Further, the linker portion appears to have a definitive structure, which is independent of the globular N-domain. This definitive linker Is roughly divided into two short strands, -D(65)GTTSP(70)- and -G(71)LK(73)- which are bent around -T(67)TSPG(71)- at angle of approximately 60 degrees. This bending motif of the linker may function to orient the two ice-binding sites of the N- and C-domains of RD3 in the same direction, leading to their simultaneous interactions with the ice crystal surface.