 |
PDBsum entry 2ot3
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Protein transport
|
PDB id
|
|
|
|
2ot3
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structural basis for rab gtpase activation by vps9 domain exchange factors.
|
|
|
Authors
|
|
A.Delprato,
D.G.Lambright.
|
|
|
Ref.
|
|
Nat Struct Mol Biol, 2007,
14,
406-412.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
RABEX-5 and other exchange factors with VPS9 domains regulate endocytic
trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22.
Here we report the crystal structure of the RABEX-5 catalytic core in complex
with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway.
The structure reveals how VPS9 domain exchange factors recognize Rab GTPase
substrates, accelerate GDP release and stabilize the nucleotide-free
conformation. We further identify an autoinhibitory element in a predicted
amphipathic helix located near the C terminus of the VPS9 domain. The
autoinhibitory element overlaps with the binding site for the multivalent
effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5.
Autoinhibition can be partially reversed by mutation of conserved residues on
the nonpolar face of the predicted amphipathic helix or by assembly of the
complex with RABAPTIN-5.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. Structure of the RABEX-5 HB-VPS9 tandem in complex
with nucleotide-free RAB21. (a) Ribbon representation. The
catalytic core of RABEX-5 consists of a helical bundle (light
brown;  HB1–
HB4),
a VPS9 domain (brown; V1–
V6)
and a C-terminal helix (dark brown; C).
RAB21 ( 1–
5
and  1–
6)
is depicted in gray with the P-loop, switch and interswitch
regions colored as indicated. (b) Docking of nonpolar residues
in the switch and interswitch regions of Rab21 in the
hydrophobic groove between the V4
and V6
helices of the VPS9 domain. RABEX-5 is depicted as a gray ribbon
with yellow side chains underneath a semitransparent surface.
RAB21 is depicted as a tube with side chains. (c) Network of
intermolecular polar interactions at the RAB21–VPS9 domain
interface. Dotted lines represent hydrogen bonds.
|
|
Figure 3.
Figure 3. Comparison with the nucleotide-free Sec7–Arf GTPase
complex. (a) Nucleotide-free RAB21 in complex with the
HB-VPS9 tandem of RABEX-5. (b) Nucleotide-free ARF1 in complex
with the Sec7 domain of Gea2 (ref. 39). The helices that
comprise the core of the GTPase-binding sites in the VPS9 and
Sec7 domains are depicted in brown. The invariant P-loop lysine
(RAB21 and ARF1), aspartic acid finger (VPS9 domain) and
glutamic acid finger (Sec7 domain) are depicted as spheres.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2007,
14,
406-412)
copyright 2007.
|
|
|
|
|
|
|
