Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics

Wu, Chun-Xiang; Liao, Jingling; Park, Yangshin; Reed, Xylena; Engel, Victoria A.; Hoang, Neo C.; Takagi, Yuichiro; Johnson, Steven M.; Wang, Mu; Federici, Mark; Nichols, R. Jeremy; Sanishvili, Ruslan; Cookson, Mark R.; Hoang, Quyen Q.

doi:10.1074/jbc.RA119.007631

Title: Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics

Abstract

Mutation in Leucine Rich Repeat Kinase 2 (LRRK2) is a common cause of familial Parkinson's disease (PD). Recently, we showed that a disease-associated mutation R1441H rendered the GTPase domain of LRRK2 catalytically less active and thereby trapping it in a more persistently "on" conformation. However, the mechanism involved and characteristics of this "on" conformation remained unknown. Here, we report that the ROC domain of LRRK2 exists in a dynamic dimermonomer equilibrium that is oppositely driven by GDP and GTP binding. We also observed that the diseaseassociated mutations at residue 1441 impair this dynamic and shift the conformation of ROC to a GTPbound- like monomeric conformation. Moreover, we show that residue arginine 1441 is critical for regulating the conformational dynamics of ROC. In summary, our results reveal that the PD-associated substitutions at Arg-1441 of LRRK2 alter monomerdimer dynamics and thereby trap its GTPase domain in an activated state.

Authors:

Wu, Chun-Xiang ^[1]; Liao, Jingling ^[2]; Park, Yangshin ^[1]; Reed, Xylena ^[3]; Engel, Victoria A. ^[1]; Hoang, Neo C. ^[1]; Takagi, Yuichiro ^[4];

^[4]; Wang, Mu ^[5]; Federici, Mark ^[6]; Nichols, R. Jeremy ^[7]; Sanishvili, Ruslan ^[8];

^[3]; Hoang, Quyen Q. ^[9]

Indiana Univ. School of Medicine, Indianapolis, IN (United States). Dept. of Biochemistry and Molecular Biology; Indiana Univ. School of Medicine, Indianapolis, IN (United States). The Stark Neurosciences Inst.
Indiana Univ. School of Medicine, Indianapolis, IN (United States). Dept. of Biochemistry and Molecular Biology; Indiana Univ. School of Medicine, Indianapolis, IN (United States). The Stark Neurosciences Inst.; Wuhan Univ. of Science and Technology School of Medicine, Wuhan (China). Dept. of Public Health
National Inst. of Health, Bethesda, MD (United States). Lab. of Neurogenetics
Indiana Univ. School of Medicine, Indianapolis, IN (United States). Dept. of Biochemistry and Molecular Biology;
Indiana Univ. School of Medicine, Indianapolis, IN (United States). Dept. of Biochemistry and Molecular Biology; Xi'an Jiaotong-Liverpool Univ., Suzhou, Jiangsu (China). Dept. of Biological Sciences
ThermoFisher Scientific, Carlsbad (California)
Stanford Univ., Stanford, CA (United States). Dept. of Pathology
Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Sciences Division
Indiana Univ. School of Medicine, Indianapolis, IN (United States). Dept. of Biochemistry and Molecular Biology and Neurology; Indiana Univ. School of Medicine, Indianapolis, IN (United States). The Stark Neurosciences Inst.

Publication Date:: Fri Feb 22 00:00:00 EST 2019

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:: National Science Foundation (NSF)

OSTI Identifier:: 1571497

Grant/Contract Number:: AC02-06CH11357

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Biological Chemistry

Additional Journal Information:: Journal Volume: 294; Journal Issue: 15; Journal ID: ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular Biology

Country of Publication:: United States

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; GTPase; Parkinson's disease; Ras of complex proteins (ROC); conformational dynamics; disease mutation; enzyme activation; kinase; leucine-rich repeat kinase 2 (LRRK2); neurodegeneration

Citation Formats


                    Wu, Chun-Xiang, Liao, Jingling, Park, Yangshin, Reed, Xylena, Engel, Victoria A., Hoang, Neo C., Takagi, Yuichiro, Johnson, Steven M., Wang, Mu, Federici, Mark, Nichols, R. Jeremy, Sanishvili, Ruslan, Cookson, Mark R., and Hoang, Quyen Q. Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics.  United States: N. p., 2019. 
Web.  doi:10.1074/jbc.RA119.007631.

Copy to clipboard


                    Wu, Chun-Xiang, Liao, Jingling, Park, Yangshin, Reed, Xylena, Engel, Victoria A., Hoang, Neo C., Takagi, Yuichiro, Johnson, Steven M., Wang, Mu, Federici, Mark, Nichols, R. Jeremy, Sanishvili, Ruslan, Cookson, Mark R., & Hoang, Quyen Q. Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics.  United States.  https://doi.org/10.1074/jbc.RA119.007631

Copy to clipboard


                    Wu, Chun-Xiang, Liao, Jingling, Park, Yangshin, Reed, Xylena, Engel, Victoria A., Hoang, Neo C., Takagi, Yuichiro, Johnson, Steven M., Wang, Mu, Federici, Mark, Nichols, R. Jeremy, Sanishvili, Ruslan, Cookson, Mark R., and Hoang, Quyen Q. Fri .  
"Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics".  United States.  https://doi.org/10.1074/jbc.RA119.007631.  https://www.osti.gov/servlets/purl/1571497.

Copy to clipboard


                    
@article{osti_1571497,

  title        = {Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics},

  author       = {Wu, Chun-Xiang and Liao, Jingling and Park, Yangshin and Reed, Xylena and Engel, Victoria A. and Hoang, Neo C. and Takagi, Yuichiro and Johnson, Steven M. and Wang, Mu and Federici, Mark and Nichols, R. Jeremy and Sanishvili, Ruslan and Cookson, Mark R. and Hoang, Quyen Q.},

  abstractNote = {Mutation in Leucine Rich Repeat Kinase 2 (LRRK2) is a common cause of familial Parkinson's disease (PD). Recently, we showed that a disease-associated mutation R1441H rendered the GTPase domain of LRRK2 catalytically less active and thereby trapping it in a more persistently "on" conformation. However, the mechanism involved and characteristics of this "on" conformation remained unknown. Here, we report that the ROC domain of LRRK2 exists in a dynamic dimermonomer equilibrium that is oppositely driven by GDP and GTP binding. We also observed that the diseaseassociated mutations at residue 1441 impair this dynamic and shift the conformation of ROC to a GTPbound- like monomeric conformation. Moreover, we show that residue arginine 1441 is critical for regulating the conformational dynamics of ROC. In summary, our results reveal that the PD-associated substitutions at Arg-1441 of LRRK2 alter monomerdimer dynamics and thereby trap its GTPase domain in an activated state.},

  doi          = {10.1074/jbc.RA119.007631},

  journal      = {Journal of Biological Chemistry},

  number       = 15,

  volume       = 294,

  place        = {United States},

  year         = {Fri Feb 22 00:00:00 EST 2019},

  month        = {Fri Feb 22 00:00:00 EST 2019}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1074/jbc.RA119.007631

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 15 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

GTP Binding Is Essential to the Protein Kinase Activity of LRRK2, a Causative Gene Product for Familial Parkinson's Disease ^†
journal, February 2007

Ito, Genta; Okai, Takuro; Fujino, Go
Biochemistry, Vol. 46, Issue 5
DOI: 10.1021/bi061960m

Parkinson's disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity
journal, January 2007

West, Andrew B.; Moore, Darren J.; Choi, Catherine
Human Molecular Genetics, Vol. 16, Issue 2
DOI: 10.1093/hmg/ddl471

Mutations in LRRK2 Cause Autosomal-Dominant Parkinsonism with Pleomorphic Pathology
journal, November 2004

Zimprich, Alexander; Biskup, Saskia; Leitner, Petra
Neuron, Vol. 44, Issue 4
DOI: 10.1016/j.neuron.2004.11.005

The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease
journal, November 2010

Cookson, Mark R.
Nature Reviews Neuroscience, Vol. 11, Issue 12
DOI: 10.1038/nrn2935

The R1441C mutation of LRRK2 disrupts GTP hydrolysis
journal, June 2007

Lewis, Patrick A.; Greggio, Elisa; Beilina, Alexandra
Biochemical and Biophysical Research Communications, Vol. 357, Issue 3
DOI: 10.1016/j.bbrc.2007.04.006

Cloning of the Gene Containing Mutations that Cause PARK8-Linked Parkinson's Disease
journal, November 2004

Paisán-Ruı́z, Coro; Jain, Shushant; Evans, E. Whitney
Neuron, Vol. 44, Issue 4
DOI: 10.1016/j.neuron.2004.10.023

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase
journal, September 2008

Gotthardt, Katja; Weyand, Michael; Kortholt, Arjan
The EMBO Journal, Vol. 27, Issue 17
DOI: 10.1038/emboj.2008.167

A homologue of the Parkinson’s disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover
journal, October 2017

Deyaert, Egon; Wauters, Lina; Guaitoli, Giambattista
Nature Communications, Vol. 8, Issue 1
DOI: 10.1038/s41467-017-01103-4

LRRK2 in Parkinson's disease: protein domains and functional insights
journal, May 2006

Mata, Ignacio F.; Wedemeyer, William J.; Farrer, Matthew J.
Trends in Neurosciences, Vol. 29, Issue 5
DOI: 10.1016/j.tins.2006.03.006

LRRK2 autophosphorylation enhances its GTPase activity
journal, January 2016

Liu, Zhiyong; Mobley, James A.; DeLucas, Lawrence J.
The FASEB Journal, Vol. 30, Issue 1
DOI: 10.1096/fj.15-277095

Roco Proteins and the Parkinson’s Disease-Associated LRRK2
journal, December 2018

Liao, Jingling; Hoang, Quyen
International Journal of Molecular Sciences, Vol. 19, Issue 12
DOI: 10.3390/ijms19124074

Mutations in <i>LRRK2</i> as a Cause of Parkinson’s Disease
journal, December 2007

Giasson, Benoit I.; Van Deerlin, Vivianna M.
Neurosignals, Vol. 16, Issue 1
DOI: 10.1159/000109764

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery
journal, December 2001

Pantoliano, M. W.; Petrella, E. C.; Kwasnoski, J. D.
Journal of Biomolecular Screening, Vol. 6, Issue 6
DOI: 10.1177/108705710100600609

The R1441C mutation alters the folding properties of the ROC domain of LRRK2
journal, December 2009

Li, Yongchao; Dunn, Laura; Greggio, Elisa
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1792, Issue 12
DOI: 10.1016/j.bbadis.2009.09.010

The Parkinson’s disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase thatstimulates kinase activity
journal, October 2007

Guo, Luxuan; Gandhi, Payal N.; Wang, Wen
Experimental Cell Research, Vol. 313, Issue 16
DOI: 10.1016/j.yexcr.2007.07.007

Kinase activity is required for the toxic effects of mutant LRRK2/dardarin
journal, August 2006

Greggio, Elisa; Jain, Shushant; Kingsbury, Ann
Neurobiology of Disease, Vol. 23, Issue 2
DOI: 10.1016/j.nbd.2006.04.001

Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain
journal, March 2014

Liao, J.; Wu, C. -X.; Burlak, C.
Proceedings of the National Academy of Sciences, Vol. 111, Issue 11
DOI: 10.1073/pnas.1323285111

Direct binding of α-actinin enhances TRPP3 channel activity
journal, December 2007

Li, Qiang; Dai, Xiao-Qing; Shen, Patrick Y.
Journal of Neurochemistry, Vol. 103, Issue 6
DOI: 10.1111/j.1471-4159.2007.04940.x

Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease
journal, February 2014

Beilina, A.; Rudenko, I. N.; Kaganovich, A.
Proceedings of the National Academy of Sciences, Vol. 111, Issue 7
DOI: 10.1073/pnas.1318306111

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase
journal, July 2008

Gotthardt, Katja; Weyand, Michael; Kortholt, Arjan
The EMBO Journal, Vol. 27, Issue 16
DOI: 10.1038/emboj.2008.150

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery
journal, December 2001

Pantoliano, Michael W.; Petrella, Eugene C.; Kwasnoski, Joseph D.
Journal of Biomolecular Screening, Vol. 6, Issue 6
DOI: 10.1089/108705701753364922

Similar Records in DOE PAGES and OSTI.GOV collections:

Dual arginine recognition of LRRK2 phosphorylated Rab GTPases

Journal Article Waschbüsch, Dieter ; Purlyte, Elena ; Khan, Amir R. - Biophysical Journal

Parkinson’s-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime regulators of membrane trafficking in eukaryotic cells. Rabs exert their biological effects by recruitment of effector proteins to subcellular compartments via their Rab-binding domain (RBD). Effectors are modular and typically contain additional domains that regulate various aspects of vesicle formation, trafficking, fusion, and organelle dynamics. The RBD of effectors is typically an α-helical coiled coil that recognizes the GTP conformation of the switch 1 and switch 2 motifs of Rabs. LRRK2 phosphorylates Rab8a at T72 (pT72)more »« less
https://doi.org/10.1016/j.bpj.2021.03.030

Full Text Available
Crystal structure of the WD40 domain dimer of LRRK2

Journal Article Zhang, Pengfei ; Fan, Ying ; Ru, Heng ; ... - Proceedings of the National Academy of Sciences of the United States of America

Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein with both a Ras of complex (ROC) domain and a kinase domain (KD) and, therefore, exhibits both GTPase and kinase activities. Human genetics studies have linked LRRK2 as a major genetic contributor to familial and sporadic Parkinson’s disease (PD), a neurodegenerative movement disorder that inflicts millions worldwide. The C-terminal region of LRRK2 is a Trp-Asp-40 (WD40) domain with poorly defined biological functions but has been implicated in microtubule interaction. Here, we present the crystal structure of the WD40 domain of human LRRK2 at 2.6-Å resolution, which reveals a seven-bladed WD40more »« less
Cited by 37
https://doi.org/10.1073/pnas.1817889116

Full Text Available
Parkinson's disease-associated mutant LRRK2 phosphorylates Rab7L1 and modifies trans-Golgi morphology

Journal Article Fujimoto, Tetta ; Kuwahara, Tomoki ; Eguchi, Tomoya ; ... - Biochemical and Biophysical Research Communications

Highlights: • Rab7L1 is identified as a bona fide substrate of LRRK2. • Ser72 is a major in-cell phosphorylation site of Rab7L1. • Parkinson's-linked mutations in LRRK2 increase the Ser72 phosphorylation of Rab7L1. • Rab7L1 phosphorylation at Ser72 modifies the trans-Golgi morphology. Mutations in leucine-rich repeat kinase 2 (LRRK2) are the major genetic cause of autosomal-dominantly inherited Parkinson's disease. LRRK2 is implicated in the regulation of intracellular trafficking, neurite outgrowth and PD risk in connection with Rab7L1, a putative interactor of LRRK2. Recently, a subset of Rab GTPases have been reported as substrates of LRRK2. Here we examine the kinasemore »« less
https://doi.org/10.1016/J.BBRC.2017.12.024
Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2

Journal Article Waschbüsch, Dieter ; Purlyte, Elena ; Pal, Prosenjit ; ... - Structure

Rab8a is associated with the dynamic regulation of membrane protrusions in polarized cells. Rab8a is one of several Rab GTPases that are substrates of leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase that is linked to Parkinson's disease. Rab8a is phosphorylated at T72 (pT72) in its switch 2 helix and recruits the phospho-specific effector RILPL2, which subsequently regulates ciliogenesis. Here, we report the crystal structure of phospho-Rab8a (pRab8a) in complex with the RH2 (RILP homology) domain of RILPL2. The complex is a heterotetramer with RILPL2 forming a central α-helical dimer that bridges two pRab8a molecules. The N termini of themore »« less
Cited by 27
https://doi.org/10.1016/j.str.2020.01.005
Phosphorylation of p53 by LRRK2 induces microglial tumor necrosis factor α-mediated neurotoxicity

Journal Article Ho, Dong Hwan, E-mail: ethan2887@gmail.com ; Seol, Wongi ; Eun, Jin Hwan ; ... - Biochemical and Biophysical Research Communications

Leucine-rich repeat kinase (LRRK2), a major causal gene of Parkinson's disease (PD), functions as a kinase. The most prevalent mutation of LRRK2 is G2019S. It exhibits increased kinase activity compared to the wildtype LRRK2. Previous studies have shown that LRRK2 can phosphorylate p53 at T304 and T377 of threonine-X-arginine (TXR) motif in neurons. Reduction of LRRK2 expression or inhibition of LRRK2 kinase activity has been shown to be able to alleviate LPS-induced neuroinflammation in microglia cells. In this study, we found that LRRK2 could also phosphorylate p53 in microglia model BV2 cells. Transfection of BV2 with phosphomimetic p53 T304/377D significantlymore »« less
https://doi.org/10.1016/J.BBRC.2016.11.163

Similar Records

Title: Parkinson's disease-associated mutations in the GTPase domain of LRRK2 impair its nucleotide-dependent conformational dynamics

Abstract

Citation Formats

GTP Binding Is Essential to the Protein Kinase Activity of LRRK2, a Causative Gene Product for Familial Parkinson's Disease † journal, February 2007

Parkinson's disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity journal, January 2007

Mutations in LRRK2 Cause Autosomal-Dominant Parkinsonism with Pleomorphic Pathology journal, November 2004

The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease journal, November 2010

The R1441C mutation of LRRK2 disrupts GTP hydrolysis journal, June 2007

Cloning of the Gene Containing Mutations that Cause PARK8-Linked Parkinson's Disease journal, November 2004

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase journal, September 2008

A homologue of the Parkinson’s disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover journal, October 2017

LRRK2 in Parkinson's disease: protein domains and functional insights journal, May 2006

LRRK2 autophosphorylation enhances its GTPase activity journal, January 2016

Roco Proteins and the Parkinson’s Disease-Associated LRRK2 journal, December 2018

Mutations in <i>LRRK2</i> as a Cause of Parkinson’s Disease journal, December 2007

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery journal, December 2001

The R1441C mutation alters the folding properties of the ROC domain of LRRK2 journal, December 2009

The Parkinson’s disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase thatstimulates kinase activity journal, October 2007

Kinase activity is required for the toxic effects of mutant LRRK2/dardarin journal, August 2006

Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain journal, March 2014

Direct binding of α-actinin enhances TRPP3 channel activity journal, December 2007

Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease journal, February 2014

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase journal, July 2008

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery journal, December 2001

GTP Binding Is Essential to the Protein Kinase Activity of LRRK2, a Causative Gene Product for Familial Parkinson's Disease ^†
journal, February 2007

Parkinson's disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity
journal, January 2007

Mutations in LRRK2 Cause Autosomal-Dominant Parkinsonism with Pleomorphic Pathology
journal, November 2004

The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease
journal, November 2010

The R1441C mutation of LRRK2 disrupts GTP hydrolysis
journal, June 2007

Cloning of the Gene Containing Mutations that Cause PARK8-Linked Parkinson's Disease
journal, November 2004

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase
journal, September 2008

A homologue of the Parkinson’s disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover
journal, October 2017

LRRK2 in Parkinson's disease: protein domains and functional insights
journal, May 2006

LRRK2 autophosphorylation enhances its GTPase activity
journal, January 2016

Roco Proteins and the Parkinson’s Disease-Associated LRRK2
journal, December 2018

Mutations in <i>LRRK2</i> as a Cause of Parkinson’s Disease
journal, December 2007

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery
journal, December 2001

The R1441C mutation alters the folding properties of the ROC domain of LRRK2
journal, December 2009

The Parkinson’s disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase thatstimulates kinase activity
journal, October 2007

Kinase activity is required for the toxic effects of mutant LRRK2/dardarin
journal, August 2006

Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain
journal, March 2014

Direct binding of α-actinin enhances TRPP3 channel activity
journal, December 2007

Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease
journal, February 2014

Structure of the Roc–COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase
journal, July 2008

High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery
journal, December 2001