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Title: p190RhoGAP proteins contain pseudoGTPase domains

Abstract

The two p190RhoGAP proteins, p190RhoGAP-A and -B, are key regulators of Rho GTPase signaling and are essential for actin cytoskeletal structure and contractility. Here we report the discovery of two evolutionarily conserved GTPase-like domains located in the ‘middle domain’, previously thought to be unstructured. Deletion of these domains reduces RhoGAP activity. Crystal structures, MANT-GTPγS binding, thermal denaturation, biochemical assays and sequence homology analysis all strongly support defects in nucleotide-binding activity. Analysis of p190RhoGAP proteins therefore indicates the presence of two previously unidentified domains which represent an emerging group of pseudoenzymes, the pseudoGTPases.

Authors:
 [1];  [1]
  1. Yale Univ. School of Medicine, New Haven, CT (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division; National Inst. of Health
OSTI Identifier:
1430346
Grant/Contract Number:  
[AC02-06CH11357; P41GM103403; R01NS085078; R01GM109487; R01GM114621; R01GM102262; R01GM100411; P50CA121974; S10OD018007]
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
[ Journal Volume: 8; Journal Issue: 1]; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; Hydrolases; Proteins; X-ray crystallography

Citation Formats

Stiegler, Amy L., and Boggon, Titus J. p190RhoGAP proteins contain pseudoGTPase domains. United States: N. p., 2017. Web. doi:10.1038/s41467-017-00483-x.
Stiegler, Amy L., & Boggon, Titus J. p190RhoGAP proteins contain pseudoGTPase domains. United States. doi:10.1038/s41467-017-00483-x.
Stiegler, Amy L., and Boggon, Titus J. Mon . "p190RhoGAP proteins contain pseudoGTPase domains". United States. doi:10.1038/s41467-017-00483-x. https://www.osti.gov/servlets/purl/1430346.
@article{osti_1430346,
title = {p190RhoGAP proteins contain pseudoGTPase domains},
author = {Stiegler, Amy L. and Boggon, Titus J.},
abstractNote = {The two p190RhoGAP proteins, p190RhoGAP-A and -B, are key regulators of Rho GTPase signaling and are essential for actin cytoskeletal structure and contractility. Here we report the discovery of two evolutionarily conserved GTPase-like domains located in the ‘middle domain’, previously thought to be unstructured. Deletion of these domains reduces RhoGAP activity. Crystal structures, MANT-GTPγS binding, thermal denaturation, biochemical assays and sequence homology analysis all strongly support defects in nucleotide-binding activity. Analysis of p190RhoGAP proteins therefore indicates the presence of two previously unidentified domains which represent an emerging group of pseudoenzymes, the pseudoGTPases.},
doi = {10.1038/s41467-017-00483-x},
journal = {Nature Communications},
number = [1],
volume = [8],
place = {United States},
year = {2017},
month = {9}
}

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Works referenced in this record:

A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties
journal, December 2013

  • Murphy, James M.; Zhang, Qingwei; Young, Samuel N.
  • Biochemical Journal, Vol. 457, Issue 2
  • DOI: 10.1042/BJ20131174

The evolving world of pseudoenzymes: proteins, prejudice and zombies
journal, November 2016


The InterPro protein families database: the classification resource after 15 years
journal, November 2014

  • Mitchell, Alex; Chang, Hsin-Yu; Daugherty, Louise
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1243

Cancer-associated mutations in the protrusion-targeting region of p190RhoGAP impact tumor cell migration
journal, September 2016

  • Binamé, Fabien; Bidaud-Meynard, Aurélien; Magnan, Laure
  • The Journal of Cell Biology, Vol. 214, Issue 7
  • DOI: 10.1083/jcb.201601063

Presenting your structures: the CCP 4 mg molecular-graphics software
journal, March 2011

  • McNicholas, S.; Potterton, E.; Wilson, K. S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911007281

RAC1P29S is a spontaneously activating cancer-associated GTPase
journal, January 2013

  • Davis, M. J.; Ha, B. H.; Holman, E. C.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 3
  • DOI: 10.1073/pnas.1220895110

Emerging roles of pseudokinases
journal, September 2006

  • Boudeau, Jérôme; Miranda-Saavedra, Diego; Barton, Geoffrey J.
  • Trends in Cell Biology, Vol. 16, Issue 9
  • DOI: 10.1016/j.tcb.2006.07.003

A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region
journal, October 2014

  • Schroeder, Courtney M.; Ostrem, Jonathan ML; Hertz, Nicholas T.
  • eLife, Vol. 3
  • DOI: 10.7554/eLife.03351

Regulation of the small GTP-binding protein Rho by cell adhesion and the cytoskeleton
journal, February 1999


The Ras superfamily at a glance
journal, March 2005


Rnd Proteins Function as RhoA Antagonists by Activating p190 RhoGAP
journal, July 2003


Dali server: conservation mapping in 3D
journal, May 2010

  • Holm, Liisa; Rosenstr�m, P�ivi
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq366

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Collaboration gets the most out of software
journal, September 2013


Biochemical and Structural Characterization of the Gem GTPase
journal, November 2006

  • Splingard, Anne; Ménétrey, Julie; Perderiset, Mylène
  • Journal of Biological Chemistry, Vol. 282, Issue 3
  • DOI: 10.1074/jbc.M604363200

Comparisons between the three-dimensional structures of the chemotactic protein Che Y and the normal Gly 12-p21 protein
journal, July 1990


Function and regulation of Rnd proteins
journal, January 2006

  • Chardin, Pierre
  • Nature Reviews Molecular Cell Biology, Vol. 7, Issue 1
  • DOI: 10.1038/nrm1788

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

Day of the dead: pseudokinases and pseudophosphatases in physiology and disease
journal, September 2014

  • Reiterer, Veronika; Eyers, Patrick A.; Farhan, Hesso
  • Trends in Cell Biology, Vol. 24, Issue 9
  • DOI: 10.1016/j.tcb.2014.03.008

TLSMD web server for the generation of multi-group TLS models
journal, January 2006


Molecular cloning of cDNAs encoding the GAP-associated protein p190: Implications for a signaling pathway from ras to the nucleus
journal, May 1992


Fast and accurate automatic structure prediction with HHpred
journal, January 2009

  • Hildebrand, Andrea; Remmert, Michael; Biegert, Andreas
  • Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue S9
  • DOI: 10.1002/prot.22499

JPred4: a protein secondary structure prediction server
journal, April 2015

  • Drozdetskiy, Alexey; Cole, Christian; Procter, James
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv332

Insights into the GTP/GDP Cycle of RabX3, a Novel GTPase from Entamoeba histolytica with Tandem G-Domains
journal, February 2014

  • Chandra, Mintu; Mukherjee, Madhumita; Srivastava, Vijay Kumar
  • Biochemistry, Vol. 53, Issue 7
  • DOI: 10.1021/bi401428f

p190-B, a New Member of the Rho GAP Family, and Rho Are Induced to Cluster after Integrin Cross-linking
journal, December 1995

  • Burbelo, Peter D.; Miyamoto, Shingo; Utani, Atsushi
  • Journal of Biological Chemistry, Vol. 270, Issue 52
  • DOI: 10.1074/jbc.270.52.30919

Data publication with the structural biology data grid supports live analysis
journal, March 2016

  • Meyer, Peter A.; Socias, Stephanie; Key, Jason
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10882

The HHpred interactive server for protein homology detection and structure prediction
journal, July 2005

  • Soding, J.; Biegert, A.; Lupas, A. N.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki408

Pseudokinases-remnants of evolution or key allosteric regulators?
journal, December 2010


Improved molecular replacement by density- and energy-guided protein structure optimization
journal, May 2011

  • DiMaio, Frank; Terwilliger, Thomas C.; Read, Randy J.
  • Nature, Vol. 473, Issue 7348
  • DOI: 10.1038/nature09964

The pseudo GTPase CENP-M drives human kinetochore assembly
journal, July 2014


CDD: NCBI's conserved domain database
journal, November 2014

  • Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1221

Insights into the evolution of divergent nucleotide-binding mechanisms among pseudokinases revealed by crystal structures of human and mouse MLKL
journal, January 2014

  • Murphy, James M.; Lucet, Isabelle S.; Hildebrand, Joanne M.
  • Biochemical Journal, Vol. 457, Issue 3
  • DOI: 10.1042/BJ20131270

The importance of alignment accuracy for molecular replacement
journal, June 2004

  • Schwarzenbacher, Robert; Godzik, Adam; Grzechnik, Slawomir K.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 7
  • DOI: 10.1107/S0907444904010145

Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site
journal, January 2009


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

The protein kinase family: conserved features and deduced phylogeny of the catalytic domains
journal, July 1988


A graphical user interface to the CCP 4 program suite
journal, June 2003

  • Potterton, Elizabeth; Briggs, Peter; Turkenburg, Maria
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7
  • DOI: 10.1107/S0907444903008126

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

A generic method for assignment of reliability scores applied to solvent accessibility predictions
journal, January 2009

  • Petersen, Bent; Petersen, Thomas; Andersen, Pernille
  • BMC Structural Biology, Vol. 9, Issue 1
  • DOI: 10.1186/1472-6807-9-51

Structural resemblance between the families of bacterial signal-transduction proteins and of G proteins revealed by graph theoretical techniques
journal, January 1990

  • Artymiuk, Peter J.; Rice, David W.; Mitchell, Eleanor M.
  • "Protein Engineering, Design and Selection", Vol. 4, Issue 1
  • DOI: 10.1093/protein/4.1.39

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
journal, June 2008

  • Langer, Gerrit; Cohen, Serge X.; Lamzin, Victor S.
  • Nature Protocols, Vol. 3, Issue 7
  • DOI: 10.1038/nprot.2008.91

Adhesion-Dependent Regulation of p190RhoGAP in the Developing Brain by the Abl-Related Gene Tyrosine Kinase
journal, April 2004

  • Hernández, Samuel E.; Settleman, Jeffrey; Koleske, Anthony J.
  • Current Biology, Vol. 14, Issue 8
  • DOI: 10.1016/j.cub.2004.03.062

RHO GTPASES: Biochemistry and Biology
journal, November 2005


The GTPase superfamily: conserved structure and molecular mechanism
journal, January 1991

  • Bourne, Henry R.; Sanders, David A.; McCormick, Frank
  • Nature, Vol. 349, Issue 6305
  • DOI: 10.1038/349117a0

The centaurin γ-1 GTPase-like domain functions as an NTPase
journal, January 2007

  • Soundararajan, Meera; Yang, Xiaowen; Elkins, Jonathan M.
  • Biochemical Journal, Vol. 401, Issue 3
  • DOI: 10.1042/BJ20060555

Integrin Signaling through Arg Activates p190RhoGAP by Promoting Its Binding to p120RasGAP and Recruitment to the Membrane
journal, November 2006

  • Bradley, William D.; Hernández, Samuel E.; Settleman, Jeffrey
  • Molecular Biology of the Cell, Vol. 17, Issue 11
  • DOI: 10.1091/mbc.E06-02-0132

Nucleotide-binding mechanisms in pseudokinases
journal, January 2016

  • Hammarén, Henrik M.; Virtanen, Anniina T.; Silvennoinen, Olli
  • Bioscience Reports, Vol. 36, Issue 1
  • DOI: 10.1042/BSR20150226

Scalable web services for the PSIPRED Protein Analysis Workbench
journal, June 2013

  • Buchan, Daniel W. A.; Minneci, Federico; Nugent, Tim C. O.
  • Nucleic Acids Research, Vol. 41, Issue W1
  • DOI: 10.1093/nar/gkt381

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206