FC0035
UPF2  -  UPF1

Biological function
Binding of UPF2 - UPF3 on a downstream exon junction complex (EJC) to UPF1 bound to a stalled ribosome induces nonsense-mediated decay (NMD).

Domain organization/sequence features
UPF1 is a highly conserved B120kDa protein that shows RNA-dependent ATPase and 5’ -3’ RNA helicase activities in vitro. UPF1 has a helicase domain (residues 295–914), and a highly conserved N-terminal cysteine–histidine-rich domain (CH- domain, residues 115–275) that binds three structural zinc atoms. The CH-domain contains the UPF2-binding site. UPF2 is an ~140kDa perinuclear protein characterized by three MIF4G domains. UPF3b binds to the third MIF4G domain of UPF2. The UPF1-binding region of UPF2 is at the C-terminus of the protein and is separated from the third MIF4G domain by a conserved Glu/Asp-rich acidic region.

Structural evidence
Crystal structures of the combined CH- and helicase domains (residues 115–914) of UPF1 in complex with the C-terminal region of human UPF2 (residues 1105–1198) show that UPF2 interacts with UPF1 through separated α-helical and β-hairpin elements. The C-terminal region of UPF2 is disordered in isolation and the two folded regions are formed upon binding to the UPF1 CH-domain. The N-terminal part of the UPF2 (residues 1108–1128) fragment forms a long, slightly curved, amphipathic α-helix, the C-terminal part folds into a β-hairpin (residues 1167–1189). These are connected by a 39AA long invisible linker.

Biochemical evidence
The α-helical region binds sixfold more weakly than the β-hairpin, but the combined elements bind 80-fold more tightly than the α-helical region alone. Cellular assays show that NMD is severely affected by mutations disrupting the β -hairpin binding, but not by those only affecting α-helix binding.

Mechanism category
tethering

Significance
Fuzziness enables a bipartite mode of UPF2 binding brings the ribosome and the exon-junction complex (EJC) in close proximity by forming a tight complex after an initial weak encounter with either element.