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Structural biology of the LRRK2 GTPase and kinase domains: implications for regulation.

Gilsbach BK, Kortholt A - Front Mol Neurosci (2014)

Bottom Line: Several of the pathogenic mutations in LRRK2 result in decreased GTPase activity and enhanced kinase activity, suggesting a possible PD-related gain of abnormal function.Studies with Roco proteins from the model organism Dictyostelium discoideum revealed that PD mutants have different effects and most importantly they explained the G2019S-related increased LRRK2 kinase activity.In this review we highlight the recent progress in structural and biochemical characterization of Roco proteins and discuss its implication for the understanding of the complex regulatory mechanism of LRRK2.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biochemistry, University of Groningen Groningen, Netherlands.

ABSTRACT
Human leucine rich repeat kinase 2 (LRRK2) belongs to the Roco family of proteins, which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), and a kinase domain. Mutations in LRRK2 have been found to be thus far the most frequent cause of late-onset Parkinson's disease (PD). Several of the pathogenic mutations in LRRK2 result in decreased GTPase activity and enhanced kinase activity, suggesting a possible PD-related gain of abnormal function. Important progress in the structural understanding of LRRK2 has come from our work with related Roco proteins from lower organisms. Atomic structures of Roco proteins from prokaryotes revealed that Roco proteins belong to the GAD class of molecular switches (G proteins activated by nucleotide dependent dimerization). As in LRRK2, PD-analogous mutations in Roco proteins from bacteria decrease the GTPase reaction. Studies with Roco proteins from the model organism Dictyostelium discoideum revealed that PD mutants have different effects and most importantly they explained the G2019S-related increased LRRK2 kinase activity. Furthermore, the structure of Dictyostelium Roco4 kinase in complex with the LRRK2 inhibitor H1152 showed that Roco4 and other Roco family proteins can be important for the optimization of the current, and identification of new, LRRK2 kinase inhibitors. In this review we highlight the recent progress in structural and biochemical characterization of Roco proteins and discuss its implication for the understanding of the complex regulatory mechanism of LRRK2.

No MeSH data available.


Related in: MedlinePlus

Overlay of the Dictyostelium Roco4 kinase wt, the G1179S (G2019S) and the L1180T (I2020T) structures. The wt structure is shown in red, the G1179S (G2019S) in green and the L1180T (I2020T) in light blue. Enlarged; PD mutation shown as sticks. The dashed line indicates the stabilizing hydrogen-bond.
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Figure 2: Overlay of the Dictyostelium Roco4 kinase wt, the G1179S (G2019S) and the L1180T (I2020T) structures. The wt structure is shown in red, the G1179S (G2019S) in green and the L1180T (I2020T) in light blue. Enlarged; PD mutation shown as sticks. The dashed line indicates the stabilizing hydrogen-bond.

Mentions: LRRK2 and Roco proteins are serine/threonine specific kinases. Our previous solved structure of the kinase domain of Dictyostelium Roco4 in its active and inactive state, gave insight into the regulation mechanism of this group of kinases (Gilsbach et al., 2012). Dictyostelium Roco4 has the same domain architecture as LRRK2, but is biochemically and structurally more tractable than LRRK2. Like almost all kinases, the Roco4 kinase structure consists of a canonical, two-lobed kinase structure, with an adenine nucleotide bound in the conventional nucleotide-binding pocket (Figure 2). The smaller N-terminal lobe is mostly composed of anti-parallel β sheets and contains the conserved αC-helix. The bigger C-terminal lobe mostly consists of α-helices and contains the activation loop with the conserved N-terminal DFG motif. The ATP binding site is formed by a cleft between those lobes and forms the catalytic site of the kinase together with the activation loop and αC-helix. The formation of a polar contact between Roco4 Lys 1055 from the β3-strand and Glu1078 from the αC-helix is essential for correct positioning of the αC-helix. The DFG motif is essential for catalysis: the Asp makes contact with all three ATP phosphates either directly or via coordination of a magnesium ion; the Phe makes hydrophobic contacts to the αC-helix and the HxD motif and is responsible for the correct positioning of the DFG motif. One can distinguish two conformations: a DFG-in (active) and a DFG-out (inactive) conformation. In the structure of active (phosphorylated) Roco4 kinase, the activation loop is visible and ordered. In contrast, the activation loop is not visible and is flexible in the structure of inactive (dephosphorylated) Roco4 kinase (Huse and Kuriyan, 2002; Taylor and Kornev, 2011).


Structural biology of the LRRK2 GTPase and kinase domains: implications for regulation.

Gilsbach BK, Kortholt A - Front Mol Neurosci (2014)

Overlay of the Dictyostelium Roco4 kinase wt, the G1179S (G2019S) and the L1180T (I2020T) structures. The wt structure is shown in red, the G1179S (G2019S) in green and the L1180T (I2020T) in light blue. Enlarged; PD mutation shown as sticks. The dashed line indicates the stabilizing hydrogen-bond.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4017136&req=5

Figure 2: Overlay of the Dictyostelium Roco4 kinase wt, the G1179S (G2019S) and the L1180T (I2020T) structures. The wt structure is shown in red, the G1179S (G2019S) in green and the L1180T (I2020T) in light blue. Enlarged; PD mutation shown as sticks. The dashed line indicates the stabilizing hydrogen-bond.
Mentions: LRRK2 and Roco proteins are serine/threonine specific kinases. Our previous solved structure of the kinase domain of Dictyostelium Roco4 in its active and inactive state, gave insight into the regulation mechanism of this group of kinases (Gilsbach et al., 2012). Dictyostelium Roco4 has the same domain architecture as LRRK2, but is biochemically and structurally more tractable than LRRK2. Like almost all kinases, the Roco4 kinase structure consists of a canonical, two-lobed kinase structure, with an adenine nucleotide bound in the conventional nucleotide-binding pocket (Figure 2). The smaller N-terminal lobe is mostly composed of anti-parallel β sheets and contains the conserved αC-helix. The bigger C-terminal lobe mostly consists of α-helices and contains the activation loop with the conserved N-terminal DFG motif. The ATP binding site is formed by a cleft between those lobes and forms the catalytic site of the kinase together with the activation loop and αC-helix. The formation of a polar contact between Roco4 Lys 1055 from the β3-strand and Glu1078 from the αC-helix is essential for correct positioning of the αC-helix. The DFG motif is essential for catalysis: the Asp makes contact with all three ATP phosphates either directly or via coordination of a magnesium ion; the Phe makes hydrophobic contacts to the αC-helix and the HxD motif and is responsible for the correct positioning of the DFG motif. One can distinguish two conformations: a DFG-in (active) and a DFG-out (inactive) conformation. In the structure of active (phosphorylated) Roco4 kinase, the activation loop is visible and ordered. In contrast, the activation loop is not visible and is flexible in the structure of inactive (dephosphorylated) Roco4 kinase (Huse and Kuriyan, 2002; Taylor and Kornev, 2011).

Bottom Line: Several of the pathogenic mutations in LRRK2 result in decreased GTPase activity and enhanced kinase activity, suggesting a possible PD-related gain of abnormal function.Studies with Roco proteins from the model organism Dictyostelium discoideum revealed that PD mutants have different effects and most importantly they explained the G2019S-related increased LRRK2 kinase activity.In this review we highlight the recent progress in structural and biochemical characterization of Roco proteins and discuss its implication for the understanding of the complex regulatory mechanism of LRRK2.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biochemistry, University of Groningen Groningen, Netherlands.

ABSTRACT
Human leucine rich repeat kinase 2 (LRRK2) belongs to the Roco family of proteins, which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), and a kinase domain. Mutations in LRRK2 have been found to be thus far the most frequent cause of late-onset Parkinson's disease (PD). Several of the pathogenic mutations in LRRK2 result in decreased GTPase activity and enhanced kinase activity, suggesting a possible PD-related gain of abnormal function. Important progress in the structural understanding of LRRK2 has come from our work with related Roco proteins from lower organisms. Atomic structures of Roco proteins from prokaryotes revealed that Roco proteins belong to the GAD class of molecular switches (G proteins activated by nucleotide dependent dimerization). As in LRRK2, PD-analogous mutations in Roco proteins from bacteria decrease the GTPase reaction. Studies with Roco proteins from the model organism Dictyostelium discoideum revealed that PD mutants have different effects and most importantly they explained the G2019S-related increased LRRK2 kinase activity. Furthermore, the structure of Dictyostelium Roco4 kinase in complex with the LRRK2 inhibitor H1152 showed that Roco4 and other Roco family proteins can be important for the optimization of the current, and identification of new, LRRK2 kinase inhibitors. In this review we highlight the recent progress in structural and biochemical characterization of Roco proteins and discuss its implication for the understanding of the complex regulatory mechanism of LRRK2.

No MeSH data available.


Related in: MedlinePlus