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PDBsum entry 3d6t
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References listed in PDB file
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Key reference
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Title
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Structure of the roc domain from the parkinson'S disease-Associated leucine-Rich repeat kinase 2 reveals a dimeric gtpase.
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Authors
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J.Deng,
P.A.Lewis,
E.Greggio,
E.Sluch,
A.Beilina,
M.R.Cookson.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
1499-1504.
[DOI no: ]
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PubMed id
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Abstract
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Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of
Parkinson's disease (PD). LRRK2 contains a Ras of complex proteins (ROC) domain
that may act as a GTPase to regulate its protein kinase activity. The structure
of ROC and the mechanism(s) by which it regulates kinase activity are not known.
Here, we report the crystal structure of the LRRK2 ROC domain in complex with
GDP-Mg(2+) at 2.0-A resolution. The structure displays a dimeric fold generated
by extensive domain-swapping, resulting in a pair of active sites constructed
with essential functional groups contributed from both monomers. Two
PD-associated pathogenic residues, R1441 and I1371, are located at the interface
of two monomers and provide exquisite interactions to stabilize the ROC dimer.
The structure demonstrates that loss of stabilizing forces in the ROC dimer is
likely related to decreased GTPase activity resulting from mutations at these
sites. Our data suggest that the ROC domain may regulate LRRK2 kinase activity
as a dimer, possibly via the C-terminal of ROC (COR) domain as a molecular
hinge. The structure of the LRRK2 ROC domain also represents a signature from a
previously undescribed class of GTPases from complex proteins and results may
provide a unique molecular target for therapeutics in PD.
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Figure 1.
The unique dimeric ROC GTPase. (A) Stereoview of the
domain-swapped dimer. The two individual monomers are shown in
yellow and green. The GDP-Mg^2+ ligands are shown in
ball-and-stick format. (B) Ribbon representation of a single
monomer. The three head, neck, and body subdomains are
indicated, along with the labeled secondary structures. The
P-loop, G3/Switch II, and G4 and G5 loops are indicated in
orange, pink, red, and cyan, respectively. The disordered G2
loop is shown as a black dotted curve. (C) Surface
representation highlighting the GDP-Mg^2+ binding pocket on the
surface of the dimer that is contributed from both monomers. The
pair of functional units are shown as ROCs1 and ROCs2,
respectively.
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Figure 2.
Structural basis of PD-associated mutations in ROC. (A) R1441
and W1434 from one monomer together with F1401 and P1406 from
the other stack on each other alternately, forming a hydrophobic
zipper at the dimer interface. The guanidinium group of R1441
also is hydrogen-bonded with the backbone carbonyl oxygen of
F1401 and the hydroxyl group of T1404 on helix α2 from the
other peptide chain. 2mF [o] − DF [c] electron density map is
shown in blue. (B) I1371 is inserted in a hydrophobic cavity,
which is constructed by residues from both monomers at the dimer
interface. I1371 is shown in stick format and colored in orange.
The surrounding residues are shown in stick format within the
semitransparent surface representation. The color scheme is the
same as that in Fig. 1. Note the side-chain methyl group of
T1404 is pointing directly to the tip of I1371, forming a
favorable van der Waals' interaction. (C) R1441C (lane 3), as a
prototypical mutation at the dimer interface, decreases
interaction with the full-length wild-type LRRK2 protein
compared with wild-type GST fusions (lane 2); no interaction was
seen with GST alone (lane 1). (D) Pull-down assays were
quantified and corrected for the amount of LRRK2 protein in the
inputs (middle blots). *, P < 0.0001; **, P < 0.01 compared with
GST alone (one-way ANOVA with Student–Newman–Kuell's post
hoc test; n = 3).
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