Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Abstract

U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.

SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns

“…The SPF45 protein contains a G-patch motif for the interactions with proteins and nucleic acids (Silverman et al, 2004;Svec et al, 2004), and C-terminal U2AF-homology motif (UHM) that binds the UHM-Ligand motifs (ULM) of its partner proteins. The binding between the UHM and the ULM plays an essential role in the splicing reactions; for instance, interaction between U2AF 65 and SF3b155 (SF3B1 as HGNC approved symbols) component of U2 snRNP (Reviewed in Loerch and Kielkopf, 2016). Remarkably, the UHM of SPF45 was shown to bind directly with ULM of both U2AF 65 and SF3b155 using the purified recombinant proteins (Corsini et al, 2007).…”

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

“…U2AF2 initially binds SF1, which is the first protein to recognize a branch point sequence (BPS) of the pre-mRNA (reviewed in [39]). Subsequently at the transition to the “A-complex”, U2AF2 associates with a “U2AF Ligand Motif” region of SF3B1 (reviewed in [40]), displacing SF1. The U2 snRNA anneals with the BPS [41], which ultimately offers the nucleophile for the first step of the splicing reaction.…”

“…The U2AF1 hotspots are located in two CCCH-type zinc knuckles that surround the U2AF2-heterodimerization motif (UHM, [40]), namely S34 is in the N-terminal ZnK1 and Q157 in the C-terminal ZnK2 (Figure 1A). Until recently, ZnK–RNA complexes were limited to two structures: an NMR structure of TIS11d, which comprises tandem ZnK1 and ZnK2 bound to an AU-rich mRNA regulatory element [66], and a 1.7 Å resolution crystal structure of the alternative splicing regulator MBNL1, which comprises a GCU-containing RNA bound to tandem ZnK1 and ZnK2 (formally ZnK3 and ZnK4 in the intact MBNL1 protein sequence) [67].…”

U2 AF 65 assemblies drive sequence‐specific splice site recognition

“…The U2AF large subunit (U2AF 65 ) binds the polypyrimidine tract (PPT) through its tandem RNA recognition motifs (RRM) [3,[6][7][8]. U2AF 65 also possesses a C-terminal atypical RRM motif called "U2AF Homology Motif" (UHM) [9,10] ( Fig 1B). This atypical RRM has lost its RNA-binding ability, but it interacts with an N-terminal "UHM Ligand Motif" (ULM) of SF1 [11][12][13].…”