Structure of Rab GDP-Dissociation Inhibitor in Complex with Prenylated YPT1 GTPase

Abstract

Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.

C3 exoenzymes, novel insights into structure and action of Rho-ADP-ribosylating toxins

“…Although C3bot does not directly interact with the guanine diphosphate, it stabilizes nucleotide binding indirectly through its interaction with the switch II region of Ral. A similar mode of nucleotide stabilization had been observed previously for two GDIs of the Rab family proteins (Rak et al 2003(Rak et al , 2004) and for RhoGDI (Hoffman et al 2000), suggesting that C3bot could act to Ral in a GDI-like manner. A structural comparison of known GDI complexes with Ral amd C3bot is shown in Fig.…”

Diels–Alder Ligation of Peptides and Proteins

“…Therefore, differently and site-specific labeled Rab proteins are considered versatile probes for the study of such biological events. [110][111][112][113][114] Rab7 (207 AA): MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQ IWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPF VVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV ELYNEFPEPIKLDKNERAKASAESCSC Figure 32. Structural details for Rab7 protein complexed with GNP and magnesium ion.…”

“…[110] The method uses a genetically engineered intein and a chitin binding domain (CBD) as fusion partners to express and purify the desired Rab thioester (Section 2.6.1) and has been successfully applied for the semi-synthesis of fluorescent labeled and lipidated Rab proteins by the groups of Dr. Kirill Alexandrov and Prof. Dr. Herbert Waldmann. [110][111][112][113][114] For the dienyl linker construction, three different cysteinyl hexadiene linkers 57, 58…”

“…This behavior was also formerly observed during the semisynthesis of lipidaded Rab proteins. [111][112][113] The purification of the Rab protein 64 ( Figure 37) was performed following the procedure described for the isolation of semisynthetic prenylated Rab proteins. [111] After incubation of the Rab hexadienyl ester 63 with the maleimide, the resulting protein precipitate was separated by centrifugation and washed with methanol in order to remove the excess of unligated dienophile.…”

Potential molecular mechanisms for fruiting body formation of Cordyceps illustrated in the case ofCordyceps sinensis

“…GTP-binding protein Ran belongs to the superfamily of Ras proteins and is crucial regulator of adenylyl cyclase (Schlenstedt et al 1997; Seewald et al 2003). Rab GDP-dissociation inhibitor (RabGDI) is a key regulator of Rab/Ypt GTPases that controls the distribution of active GTP and inactive GDP-bound forms between membranes and cytosol (Rak et al 2003). Actually, RabGDI was up-regulated in the fruiting body of C. sinensis (Table 2).…”