Structural Basis for Recruitment of Rab6-Interacting Protein 1 to Golgi via a RUN Domain

Abstract

Small GTPase Rab6 regulates vesicle trafficking at the level of Golgi via recruitment of numerous and unrelated effectors. The crystal structure of Rab6a(GTP) in complex with a 378-residue internal fragment of the effector Rab6IP1 was solved at 3.2 angstroms resolution. This Rab6IP1 region encompasses an all alpha-helical RUN domain followed in tandem by a PLAT domain that adopts a beta sandwich fold. The structure reveals that the first and last alpha helices of the RUN domain mediate binding to switch I, switch II, and the interswitch region of Rab6. It represents the largest Rab-effector complex determined to date. Comparisons with the recent structure of Rab6 in complex with an unrelated effector, human golgin GCC185, reveals significant conformational changes in the conserved hydrophobic triad of Rab6. Flexibility in the switch and interswitch regions of Rab6 mediates recognition of compositionally distinct alpha-helical coiled coils, thereby contributing to Rab6 promiscuity in effector recruitment.

Genome-wide Investigation of the Rab Binding Activity of RUN Domains: Development of a Novel Tool that Specifically Traps GTP-Rab35

“…2). The first RUN domain of DENND5A (i.e., DENND5A-RUN1), but not its second RUN domain (RUN2), interacted specifically with the CA form of Rab6A and Rab6B, consistent with a previous report (Recacha et al, 2009). DENND5B, a DENND5A-related protein, also interacted specifically, but weakly, with the CA form of Rab6A and Rab6B through the RUN1 domain (Fig.…”

“…As examples, RUNDC3A/ RPIP8 and RUFY3 (RUN and FYVE domain-containing 3)/ RPIPX/SINGAR1 (referred to as RUFY3 below) interact with Rap2 through their N-terminal domain containing the RUN domain (Janoueix-Lerosey et al, 1998;KukimotoNiino et al, 2006). Rab6IP1 (Rab6-interacting protein 1)/ DENND5A, a DENN (differentially expressed in normal and neoplastic) domain-containing protein implicated in Rab regulation (Levivier et al, 2001;Yoshimura et al, 2010), interacts with Rab6A through the first RUN domain (Recacha et al, 2009), and IPORIN (interacting protein of rab1)/RUSC2 (RUN and SH3 domain-containing 2) interacts with Rab1 through the RUN domain (Bayer et al, 2005). In addition, several RUN domain-containing proteins (simply referred to as RUN proteins below) include a TBC (Tre-2/Bub2/Cdc16) domain, which is a putative Rab-GAP (GTPase-activating protein) domain (Bernards, 2003;Fukuda, 2011;Yang et al, 2007), and RUTBC3/ RABGAP5/DJ1042K10.2/CIP85 interacts with Rab5 isoforms through its TBC domain (Haas et al, 2005;.…”

Structure-Function Analyses of the Small GTPase Rab35 and Its Effector Protein Centaurin-β2/ACAP2 during Neurite Outgrowth of PC12 Cells

“…In an attempt to identify the structural determinant responsible for the exclusive Rab35 binding specificity of centaurin-␤2, we first focused on the switch II region of Rabs that interact with most of the Rab35BPs (Fig. 1A) because several amino acids in the switch II region of certain Rabs have previously been shown to be responsible for specific effector binding (32)(33)(34)(35)(36)(37)(38). Because Rab1A/B, Rab8A/B, Rab10, Rab13, Rab15, and Rab35 are phylogenetically similar and belong to the same large branch in the phylogenetic tree (39), the amino acid sequences of their switch II region are highly conserved.…”

Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins

“…1A). 34,35 In addition, the central region of FYCO1 is predicted to form several coiled-coil domains, which mediate the dimerization of FYCO1, and are also reported to interact with the microtubule plus end-directed kinesin motor KIF5B and the small GTPase RAB7. 18,24,36 The C-terminal region of FYCO1 consists of a phosphatidylinositol-3-phosphate (PtdIns3P) lipid-binding FYVE domain, a LIR motif, and a following globular GOLD domain with unknown function.…”