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Cited by 70Protein Kinase Regulation and GTPase SignalingCellular transport and secretionProtein Structure and Dynamics

Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms

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Hanawa-Suetsugu, Kyoko, Kukimoto-Niino, Mutsuko, Mishima-Tsumagari, Chiemi, Akasaka, Ryogo, Ohsawa, Noboru, Sekine, Shun-ichi, Ito, Takuhiro, Tochio, Naoya +11 more·2012·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1113512109PMC PMC3295310
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Abstract

DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2–engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment and the C-terminal 196-residue fragment of human DOCK2 and ELMO1, respectively, as the mutual binding regions, and solved the crystal structure of their complex at 2.1-Å resolution. The C-terminal Pro-rich tail of ELMO1 winds around the Src-homology 3 domain of DOCK2, and an intermolecular five-helix bundle is formed. Overall, the entire regions of both DOCK2 and ELMO1 assemble to create a rigid structure, which is required for the DOCK2•ELMO1 binding, as revealed by mutagenesis. Intriguingly, the DOCK2•ELMO1 interface hydrophobically buries a residue which, when mutated, reportedly relieves DOCK180 from autoinhibition. We demonstrated that the ELMO-interacting region and the DOCK-homology region 2 guanine nucleotide exchange factor domain of DOCK2 associate with each other for the autoinhibition, and that the assembly with ELMO1 weakens the interaction, relieving DOCK2 from the autoinhibition. The interactions between the N- and C-terminal regions of ELMO1 reportedly cause its autoinhibition, and binding with a DOCK protein relieves the autoinhibition for ras homolog gene family, member G binding and membrane localization. In fact, the DOCK2•ELMO1 interface also buries the ELMO1 residues required for the autoinhibition within the hydrophobic core of the helix bundle. Therefore, the present complex structure reveals the structural basis by which DOCK2 and ELMO1 mutually relieve their autoinhibition for the activation of Rac1 for lymphocyte chemotaxis.

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  • DOCK families A and B contain N-terminal SH3 domains and a C-terminal proline-rich region that bind each other to maintain autoinhibition, which is alleviated upon binding adaptor proteins such as ELMO1.

    “Generally DOCK families A and B contain N-terminal SRC Homology 3 (SH3) domains and a C-terminal proline-rich region that bind each other to maintain the protein in an autoinhibited state, an interaction that is alleviated upon binding adaptor proteins such as engulfment and cell motility protein 1 (ELMO1) (36, 37).”

    From RHO to the DOCK for GDP disembarking: Structural insights into the DOCK GTPase nucleotide exchange factors (2021) · cites this paper as [37]

    The Abstract and Results identify an N-terminal SH3 domain in DOCK2 and show that ELMO1 binding relieves DOCK2 autoinhibition. But the Results identify the proline-rich tail as part of ELMO1, not DOCK2; the DOCK2 regions that associate during autoinhibition are its N-terminal ELMO-interacting region and C-terminal DHR-2-containing region. The paper therefore does not support the claimed intramolecular SH3–proline-rich interaction in DOCK proteins. (LLM, conf=0.88)

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  1. [1]Nishihara H, et al. Non-adherent cell-specific expression of DOCK2, a member of the human CDM-family proteins. Biochim Biophys Acta. 1999;1452:179–187. doi: 10.1016/s0167-4889(99)00133-0. [DOI] [PubMed] [Google Scholar] · DOI
  2. [3]Sanui T, et al. DOCK2 is essential for antigen-induced translocation of TCR and lipid rafts, but not PKC-theta and LFA-1, in T cells. Immunity. 2003;19:119–129. doi: 10.1016/s1074-7613(03)00169-9. [DOI] [PubMed] [Google Scholar] · DOI
  3. [4]Jiang H, et al. Deletion of DOCK2, a regulator of the actin cytoskeleton in lymphocytes, suppresses cardiac allograft rejection. J Exp Med. 2005;202:1121–1130. doi: 10.1084/jem.20050911. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  4. [5]Tanaka Y, et al. T helper type 2 differentiation and intracellular trafficking of the interleukin 4 receptor-alpha subunit controlled by the Rac activator Dock2. Nat Immunol. 2007;8:1067–1075. doi: 10.1038/ni1506. [DOI] [PubMed] [Google Scholar] · DOI
  5. [6]Kunisaki Y, et al. DOCK2 is a Rac activator that regulates motility and polarity during neutrophil chemotaxis. J Cell Biol. 2006;174:647–652. doi: 10.1083/jcb.200602142. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  6. [7]Nishikimi A, et al. Sequential regulation of DOCK2 dynamics by two phospholipids during neutrophil chemotaxis. Science. 2009;324:384–387. doi: 10.1126/science.1170179. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  7. [8]Gotoh K, et al. Selective control of type I IFN induction by the Rac activator DOCK2 during TLR-mediated plasmacytoid dendritic cell activation. J Exp Med. 2010;207:721–730. doi: 10.1084/jem.20091776. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  8. [9]Côté JF, Vuori K. GEF what? Dock180 and related proteins help Rac to polarize cells in new ways. Trends Cell Biol. 2007;17:383–393. doi: 10.1016/j.tcb.2007.05.001. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  9. [11]Miyamoto Y, Yamauchi J, Sanbe A, Tanoue A. Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Rac1 and Cdc42 and regulates neurite outgrowth. Exp Cell Res. 2007;313:791–804. doi: 10.1016/j.yexcr.2006.11.017. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  10. [12]Côté JF, Motoyama AB, Bush JA, Vuori K. A novel and evolutionarily conserved PtdIns(3,4,5)P3-binding domain is necessary for DOCK180 signalling. Nat Cell Biol. 2005;7:797–807. doi: 10.1038/ncb1280. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  11. [13]Premkumar L, et al. Structural basis of membrane targeting by the Dock180 family of Rho family guanine exchange factors (Rho-GEFs) J Biol Chem. 2010;285:13211–13222. doi: 10.1074/jbc.M110.102517. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI · Paper page
  12. [14]Kulkarni K, Yang J, Zhang Z, Barford D. Multiple factors confer specific Cdc42 and Rac activation by Dock exchange factors. J Biol Chem. 2011;286:25341–25351. doi: 10.1074/jbc.M111.236455. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI · Paper page
  13. [15]Yang J, Zhang Z, Roe SM, Marshall CJ, Barford D. Activation of Rho GTPases by DOCK exchange factors is mediated by a nucleotide sensor. Science. 2009;325:1398–1402. doi: 10.1126/science.1174468. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  14. [16]Sanui T, et al. DOCK2 regulates Rac activation and cytoskeletal reorganization through interaction with ELMO1. Blood. 2003;102:2948–2950. doi: 10.1182/blood-2003-01-0173. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  15. [18]Gumienny TL, et al. CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration. Cell. 2001;107:27–41. doi: 10.1016/s0092-8674(01)00520-7. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  16. [19]Grimsley CM, et al. Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration. J Biol Chem. 2004;279:6087–6097. doi: 10.1074/jbc.M307087200. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  17. [20]Lu M, et al. PH domain of ELMO functions in trans to regulate Rac activation via Dock180. Nat Struct Mol Biol. 2004;11:756–762. doi: 10.1038/nsmb800. [DOI] [PubMed] [Google Scholar] · DOI
  18. [21]Komander D, et al. An alpha-helical extension of the ELMO1 pleckstrin homology domain mediates direct interaction to DOCK180 and is critical in Rac signaling. Mol Biol Cell. 2008;19:4837–4851. doi: 10.1091/mbc.E08-04-0345. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  19. [22]Lu M, et al. A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs. Curr Biol. 2005;15:371–377. doi: 10.1016/j.cub.2005.01.050. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  20. [23]Patel M, et al. An evolutionarily conserved autoinhibitory molecular switch in ELMO proteins regulates Rac signaling. Curr Biol. 2010;20:2021–2027. doi: 10.1016/j.cub.2010.10.028. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  21. [24]Kigawa T, Matsuda T, Yabuki T, Yokoyama S. In: Cell-free Protein Synthesis. Spirin Alexander S, Swartz James R., editors. New York: Wiley; 2007. pp. 83–97. [Google Scholar]
  22. [25]Kigawa T, et al. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics. 2004;5:63–68. doi: 10.1023/B:JSFG.0000029204.57846.7d. [DOI] [PubMed] [Google Scholar] · DOI
  23. [26]Matsuda T, et al. Improving cell-free protein synthesis for stable-isotope labeling. J Biomol NMR. 2007;37:225–229. doi: 10.1007/s10858-006-9127-5. [DOI] [PubMed] [Google Scholar] · DOI
  24. [27]Cesareni G, Panni S, Nardelli G, Castagnoli L. Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett. 2002;513:38–44. doi: 10.1016/s0014-5793(01)03307-5. [DOI] [PubMed] [Google Scholar] · DOI
  25. [28]Mayer BJ. SH3 domains: Complexity in moderation. J Cell Sci. 2001;114:1253–1263. doi: 10.1242/jcs.114.7.1253. [DOI] [PubMed] [Google Scholar] · DOI
  26. [29]Chhatriwala MK, Betts L, Worthylake DK, Sondek J. The DH and PH domains of Trio coordinately engage Rho GTPases for their efficient activation. J Mol Biol. 2007;368:1307–1320. doi: 10.1016/j.jmb.2007.02.060. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  27. [30]Wohlwend D, Strasser A, Dickmanns A, Ficner R. Structural basis for RanGTP independent entry of spliceosomal U snRNPs into the nucleus. J Mol Biol. 2007;374:1129–1138. doi: 10.1016/j.jmb.2007.09.065. [DOI] [PubMed] [Google Scholar] · DOI

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Authors
Hanawa-Suetsugu, K., Kukimoto-Niino, M., Mishima-Tsumagari, C., Akasaka, R., Ohsawa, N., Sekine, S.-I., Ito, T., Tochio, N., Koshiba, S., Kigawa, T., Terada, T., Shirouzu, M., Nishikimi, A., Uruno, T., Katakai, T., Kinashi, T., Kohda, D., Fukui, Y., & Yokoyama, S.
Affiliations
  • RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan;
  • RIKEN (JP)
  • Tokyo Institute of Technology (JP)
  • Japan Science and Technology Agency (JP)
  • Kyushu University (JP)
  • Kansai Medical University (JP)
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2012-02-13
Volume
109
Issue
9
Pages
3305-3310
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.1113512109
PMC
PMC3295310
OpenAlex
W1984010921
Cited by
70
References
3
Citations by year
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FWCI
3.09
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
Japan Society for the Promotion of Science (22790469, 24111001, 22247017)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
DOCK2, ELMO1, autoinhibition, Rac1 activation, lymphocyte chemotaxis, Src homology 3 domain, DOCK180, hydrophobic interface, crystal structure
MeSH terms
Amino Acid Sequence, Humans, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Recombinant Fusion Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Crystallography, X-Ray, src Homology Domains, Nuclear Magnetic Resonance, Biomolecular, Guanine Nucleotide Exchange Factors, GTPase-Activating Proteins, rac1 GTP-Binding Protein, Protein Interaction Mapping, Adaptor Proteins, Signal Transducing, Hydrophobic and Hydrophilic Interactions

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