Structural features in EIAV NCp11: a lentivirus nucleocapsid protein with a short linker

Lentiviral nucleocapsid proteins are a class of multifunctional proteins that play an essential role in RNA packaging and viral infectivity. They contain two CX(2)CX(4)HX(4)C zinc binding motifs connected by a basic linker of variable length. The 3D structure of a 37-aa peptide corresponding to sequence 22-58 from lentiviral EIAV nucleocapsid protein NCp11, complexed with zinc, has been determined by 2D (1)H NMR spectroscopy, simulated annealing, and molecular dynamics. The solution structure consists of two zinc binding domains held together by a five-residue basic linker Arg(38)-Ala-Pro-Lys-Val(42) that allows for spatial proximity between the two finger domains. Observed linker folding is stabilized by H bonded secondary structure elements, resulting in an Omega-shaped central region, asymmetrically centered on the linker. The conformational differences and similarities with other NC zinc binding knuckles have been systematically analyzed. The two CCHC motifs, both characterized by a peculiar Pro-Gly sequence preceding the His residue, although preserving Zn-binding geometry and chirality of other known NC proteins, exhibit local fold differences both between each other and in comparison with other previously characterized retroviral CCHC motifs.