Effectors of Rab GTPases: Rab Binding Specificity and Their Role in Coordination of Rab Function and Localization - Ras Superfamily Small G Proteins: Biology and Mechanisms 2 - page 40

3.2 Structural Features of Rab:Effector Interactions

3.2.1 Diversity of Rab Effectors

Rab effector proteins are multi-domain proteins containing at least one domain that
is responsible for the interaction with the Rab protein. To date, 22 structures of
these Rab binding domains (RBDs) of effectors in complex with Rab proteins
(representing 16 different Rab:effector complexes) have been published (Table 3.1 ,
Fig. 3.1 ). In spite of the very high structural similarity of different Rab proteins, the
minimal effector RBDs significantly vary both in size (from 3.7 kDa for EAA1 to
45.6 kDa for MyoVb) and in structural organization. Most RBDs exhibit a primarily
ʱ

-helical structure, forming either coiled-coils (Rabaptin-5, FIPs, GCC185, RILP),

ʱ -hairpins [Rabenosyn-5 Helical Domain 2 (HR2) and Heptad Repeat Domain

(HepR)], or -helical bundles (R6IP1, MyoVb). Some of the RBDs contain Zn 2+

binding subdomains that play either a scaffolding role supporting the effector
structure (Slac-2, Rabphilin-3), or they directly interact with the Rab (EEA1).
ʲ

ʱ

-sandwich subdomains can also directly interact with a Rab (OCRL1) or play a
scaffolding role (R6IP1).
As can be seen from the summary in Table 3.1 and in Fig. 3.1 , 30 % of the
effector structures display a 2:2 stoichiometry. In all these cases, an effector dimer
interacts with two Rab proteins that do not contact each other directly. The
interactions occur via a dimeric symmetrical coiled-coil, which forms two sym-
metrical Rab binding sites. The monomeric RBDs, however, generate only a single
Rab binding site (Fig. 3.1 ).
In Fig. 3.1 , representative Rab:effector structures have been grouped according
to their interacting Rab protein (one group, for example, is formed by Rabaptin-5,
EEA1, and the Helical Region 2 (HR2) of Rabenosyn-5 as they can all interact with
Rab5). The recently published structures of LidA in complex with Rab1/Rab8 are
not represented in the figure and are not further discussed in this review. This
protein indeed represents a very unusual bacterial Rab effector, also termed Rab
supereffector, because of its high affinity for Rab:GTP and Rab:GDP and its
extensive promiscuity in Rab interactions (Schoebel et al. 2011 ; Cheng
et al. 2012 ). When comparing the native Rab:effector structures, it can be clearly
seen that the RBDs interacting with the same Rab protein have large structural
differences. Rab5-specific effector structures are represented by three different
folds, a C 2 H 2 zinc finger for EAA1, a parallel homodimeric coiled-coil for
Rabaptin-5, and an -helical hairpin for Rabenosyn-5 (HR2), that exhibit structural

similarity to an antiparallel coiled-coil. The Rab6 binding golgin GCC185 is a
parallel coiled-coil. In contrast, the R6IP1 RBD is composed of two subdomains: an
ʱ

ʱ

-sandwich. Rab11 effector RBDs are represented
by the highly homologous parallel coiled-coils of FIP2 and FIP3, and a two
subdomain unit composed of two ʱ -helical bundles for MyoVb. For some effector
proteins, like the Rab27 effectors Slp2-a, Slac-2a/melanophilin, and Rabphilin-3a,
a clear structural homology can be observed. All three RBDs consist of two

-helical bundle supported by a ʲ