Crystal Structure of SEDL and Its Implications for a Genetic Disease Spondyloepiphyseal Dysplasia Tarda

Abstract

SEDL is an evolutionarily highly conserved protein in eukaryotic organisms. Deletions or point mutations in the SEDL gene are responsible for the genetic disease spondyloepiphyseal dysplasia tarda (SEDT), an X-linked skeletal disorder. SEDL has been identified as a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport. Herein, we report the 2.4 Å resolution structure of SEDL, which reveals an unexpected similarity to the structures of the N-terminal regulatory domain of two SNAREs, Ykt6p and Sec22b, despite no sequence homology to these proteins. The similarity and the presence of unusually many solvent-exposed apolar residues of SEDL suggest that it serves regulatory and/or adaptor functions through multiple protein-protein interactions. Of the four known missense mutations responsible for SEDT, three mutations (S73L, F83S, V130D) map to the protein interior, where the mutations would disrupt the structure, and the fourth (D47Y) on a surface at which the mutation may abrogate functional interactions with a partner protein.Intracellular targeting and fusion of transport vesicles in eukaryotes are tightly regulated to avoid inappropriate mixing of the contents in different compartments. Central components of the membrane fusion are the proteins denoted as SNAREs 1 (soluble N-ethylmaleimide-sensitive factor attachment receptor proteins). SNAREs constitute a superfamily of proteins that share a highly conserved sequence motif, the SNARE motif composed of 60 -70 amino acids (1). Most SNAREs are membrane proteins anchored on vesicular carriers (v-SNARE) and target organelles (t-SNARE) (1). Association of the SNARE domains between v-and t-SNAREs to form a helical bundle, termed the core complex (2), is believed to be the prime event that drives membrane fusion (3, 4). While the specific pairing of v-and t-SNAREs is one mechanism of providing the fidelity of membrane fusion, other proteins or protein complexes such as the transport protein particle (TRAPP) are known to provide further specificity by controlling the tethering process, in which a transport vesicle is properly docked on target membrane prior to pairing of SNAREs (5). TRAPP is localized to an early Golgi compartment (6) and is able to exchange the nucleotide of Ypt1p GTPase, which is an upstream event of v-and t-SNARE interactions (7,8). Recent in vitro transport studies showed that yeast TRAPP I binds COPII, the vesicle coat derived from the endoplasmic reticulum (ER), indicating that TRAPP I is the receptor for tethering COPII vesicles to Golgi membranes (6). The TRAPP complexes (TRAPP I and TRAPP II) are composed of 7-10 different polypeptides, which are highly conserved in evolution, with the yeast subunits sharing between 29 and 54% sequence identity with their human counterparts (9). The biochemical function of any of the constituent proteins is virtually unknown, although the TRAPP complex was shown to stimulate nucleotide exchange on the Ypt1p and the Ypt31/32 GTPases (10).Spond...

The Structure of the MAPK Scaffold, MP1, Bound to Its Partner, p14

“…The basis for these structural similarities is unclear, as only sec22b and Ykt6p perform similar functions. Although the direct protein partners of sedlin are unknown, the protein is a component of a multiprotein complex (34) and has been proposed to be involved in multiple protein-protein interactions (31). Similarly, the SNARE proteins are involved …”

Secretory Protein Biogenesis and Traffic in the Early Secretory Pathway

“…The multisubunit TRAPPI may serve as an organizational hub on cisGolgi membranes or vesicles to coordinate vesicle tethering and fusion events. TRAPPI interactions with the COPII subunit Sec23, with the Ypt1 GTPase and potentially with SNARE proteins (Jang et al 2002;Kim et al 2006) could link tethering and fusion stages. TRAPPI-activated Ypt1 could recruit Uso1 to Golgi membranes and as COPII vesicles emerge from the ER, Uso1 could forge a longdistance link between newly formed vesicles and acceptor membranes.…”

Identification of the Yeast R-SNARE Nyv1p as a Novel Longin Domain-containing Protein

“…The longin domain (LD) is not restricted to R-SNAREs and has been identified in a variety of proteins (Rossi et al, 2004), some of which are also involved in vesicular transport. These include subunits of the adaptin complexes (Collins et al, 2002;Heldwein et al, 2004) and SEDL/Trs20p (Jang et al, 2002), a common subunit of the transport protein particle (TRAPP)I and TRAPPII multisubunit complexes, which are required for traffic between the ER and Golgi and within the Golgi (Oka and Krieger, 2005). The function of the longin fold of Sec22b/Sec22p is unknown, but in Ykt6p the longin domain folds back and binds to the SNARE-motif of the protein (Tochio et al, 2001), and this conformation is likely to be important for chaperoning the lipid modified C terminus of the cytoplasmic form of Ykt6p in cells as well as for its localization (Fukasawa et al, 2004;Hasegawa et al, 2004).…”