Discovery of new Longin and Roadblock domains that form platforms for small GTPases in Ragulator and TRAPP-II

References

• Yoshimura S, Gerondopoulos A, Linford A, Rigden DJ, Barr FA. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. J Cell Biol 2010; 191:367 - 81; http://dx.doi.org/10.1083/jcb.201008051; PMID: 20937701
   PubMed Web of Science ®Google Scholar
• Gerondopoulos A, Langemeyer L, Liang JR, Linford A, Barr FA. BLOC-3 mutated in Hermansky-Pudlak syndrome is a Rab32/38 guanine nucleotide exchange factor. Curr Biol 2012; 22:2135 - 9; http://dx.doi.org/10.1016/j.cub.2012.09.020; PMID: 23084991
   PubMed Web of Science ®Google Scholar
• Klöpper TH, Kienle N, Fasshauer D, Munro S. Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis. BMC Biol 2012; 10:71; http://dx.doi.org/10.1186/1741-7007-10-71; PMID: 22873208
   PubMed Web of Science ®Google Scholar
• Martinez-Arca S, Rudge R, Vacca M, Raposo G, Camonis J, Proux-Gillardeaux V, et al. A dual mechanism controlling the localization and function of exocytic v-SNAREs. Proc Natl Acad Sci U S A 2003; 100:9011 - 6; http://dx.doi.org/10.1073/pnas.1431910100; PMID: 12853575
   PubMed Web of Science ®Google Scholar
• Schäfer IB, Hesketh GG, Bright NA, Gray SR, Pryor PR, Evans PR, et al. The binding of Varp to VAMP7 traps VAMP7 in a closed, fusogenically inactive conformation. Nat Struct Mol Biol 2012; 19:1300 - 9; http://dx.doi.org/10.1038/nsmb.2414; PMID: 23104059
   PubMed Web of Science ®Google Scholar
• Sun Z, Anderl F, Fröhlich K, Zhao L, Hanke S, Brügger B, et al. Multiple and stepwise interactions between coatomer and ADP-ribosylation factor-1 (Arf1)-GTP. Traffic 2007; 8:582 - 93; http://dx.doi.org/10.1111/j.1600-0854.2007.00554.x; PMID: 17451557
   PubMed Web of Science ®Google Scholar
• Wanschers B, van de Vorstenbosch R, Wijers M, Wieringa B, King SM, Fransen J. Rab6 family proteins interact with the dynein light chain protein DYNLRB1. Cell Motil Cytoskeleton 2008; 65:183 - 96; http://dx.doi.org/10.1002/cm.20254; PMID: 18044744
   PubMed Web of Science ®Google Scholar
• Levivier E, Goud B, Souchet M, Calmels TP, Mornon JP, Callebaut I. uDENN, DENN, and dDENN: indissociable domains in Rab and MAP kinases signaling pathways. Biochem Biophys Res Commun 2001; 287:688 - 95; http://dx.doi.org/10.1006/bbrc.2001.5652; PMID: 11563850
   PubMed Web of Science ®Google Scholar
• Kurzbauer R, Teis D, de Araujo ME, Maurer-Stroh S, Eisenhaber F, Bourenkov GP, et al. Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc Natl Acad Sci U S A 2004; 101:10984 - 9; http://dx.doi.org/10.1073/pnas.0403435101; PMID: 15263099
   PubMed Web of Science ®Google Scholar
• Miertzschke M, Koerner C, Vetter IR, Keilberg D, Hot E, Leonardy S, et al. Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity. EMBO J 2011; 30:4185 - 97; http://dx.doi.org/10.1038/emboj.2011.291; PMID: 21847100
   PubMed Web of Science ®Google Scholar
• Schlenker O, Hendricks A, Sinning I, Wild K. The structure of the mammalian signal recognition particle (SRP) receptor as prototype for the interaction of small GTPases with Longin domains. J Biol Chem 2006; 281:8898 - 906; http://dx.doi.org/10.1074/jbc.M512415200; PMID: 16439358
   PubMed Web of Science ®Google Scholar
• Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, et al. The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes. Cell 2008; 133:1202 - 13; http://dx.doi.org/10.1016/j.cell.2008.04.049; PMID: 18585354
   PubMed Web of Science ®Google Scholar
• Wu X, Bradley MJ, Cai Y, Kümmel D, De La Cruz EM, Barr FA, et al. Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. Proc Natl Acad Sci U S A 2011; 108:18672 - 7; http://dx.doi.org/10.1073/pnas.1110415108; PMID: 22065758
   PubMed Web of Science ®Google Scholar
• Gong R, Li L, Liu Y, Wang P, Yang H, Wang L, et al. Crystal structure of the Gtr1p-Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation. Genes Dev 2011; 25:1668 - 73; http://dx.doi.org/10.1101/gad.16968011; PMID: 21816923
   PubMed Web of Science ®Google Scholar
• Jeong JH, Lee KH, Kim YM, Kim DH, Oh BH, Kim YG. Crystal structure of the Gtr1p(GTP)-Gtr2p(GDP) protein complex reveals large structural rearrangements triggered by GTP-to-GDP conversion. J Biol Chem 2012; 287:29648 - 53; http://dx.doi.org/10.1074/jbc.C112.384420; PMID: 22807443
   PubMed Web of Science ®Google Scholar
• Zhang T, Péli-Gulli MP, Yang H, De Virgilio C, Ding J. Ego3 functions as a homodimer to mediate the interaction between Gtr1-Gtr2 and Ego1 in the ego complex to activate TORC1. Structure 2012; 20:2151 - 60; http://dx.doi.org/10.1016/j.str.2012.09.019; PMID: 23123112
   PubMed Web of Science ®Google Scholar
• Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, et al. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 2008; 320:1496 - 501; http://dx.doi.org/10.1126/science.1157535; PMID: 18497260
   PubMed Web of Science ®Google Scholar
• Marat AL, Dokainish H, McPherson PS. DENN domain proteins: regulators of Rab GTPases. J Biol Chem 2011; 286:13791 - 800; http://dx.doi.org/10.1074/jbc.R110.217067; PMID: 21330364
   PubMed Web of Science ®Google Scholar
• Nookala RK, Langemeyer L, Pacitto A, Ochoa-Montaño B, Donaldson JC, Blaszczyk BK, et al. Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer. Open Biol 2012; 2:120071; http://dx.doi.org/10.1098/rsob.120071; PMID: 22977732
   PubMed Web of Science ®Google Scholar
• Baba M, Furihata M, Hong SB, Tessarollo L, Haines DC, Southon E, et al. Kidney-targeted Birt-Hogg-Dube gene inactivation in a mouse model: Erk1/2 and Akt-mTOR activation, cell hyperproliferation, and polycystic kidneys. J Natl Cancer Inst 2008; 100:140 - 54; http://dx.doi.org/10.1093/jnci/djm288; PMID: 18182616
   PubMed Web of Science ®Google Scholar
• Li L, Kim E, Yuan H, Inoki K, Goraksha-Hicks P, Schiesher RL, et al. Regulation of mTORC1 by the Rab and Arf GTPases. J Biol Chem 2010; 285:19705 - 9; http://dx.doi.org/10.1074/jbc.C110.102483; PMID: 20457610
   PubMed Web of Science ®Google Scholar
• Tsai PC, Lee SW, Liu YW, Chu CW, Chen KY, Ho JC, et al. Afi1p functions as an Arf3p polarization-specific docking factor for development of polarity. J Biol Chem 2008; 283:16915 - 27; http://dx.doi.org/10.1074/jbc.M802550200; PMID: 18397879
   PubMed Web of Science ®Google Scholar
• Denef N, Chen Y, Weeks SD, Barcelo G, Schüpbach T. Crag regulates epithelial architecture and polarized deposition of basement membrane proteins in Drosophila. Dev Cell 2008; 14:354 - 64; http://dx.doi.org/10.1016/j.devcel.2007.12.012; PMID: 18331716
   PubMed Web of Science ®Google Scholar
• Xiong B, Bayat V, Jaiswal M, Zhang K, Sandoval H, Charng WL, et al. Crag is a GEF for Rab11 required for rhodopsin trafficking and maintenance of adult photoreceptor cells. PLoS Biol 2012; 10:e1001438; http://dx.doi.org/10.1371/journal.pbio.1001438; PMID: 23226104
   PubMed Web of Science ®Google Scholar
• Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005; 33:Web Server issue W244-8; http://dx.doi.org/10.1093/nar/gki408; PMID: 15980461
   PubMedGoogle Scholar
• Zhang D, Iyer LM, He F, Aravind L. Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. Front Genet 2012; 3:283; http://dx.doi.org/10.3389/fgene.2012.00283; PMID: 23248642
   PubMedGoogle Scholar
• Levine TP, Daniels RD, Gatta AT, Wong LH, Hayes MJ. The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. Bioinformatics 2013; 29:499 - 503; http://dx.doi.org/10.1093/bioinformatics/bts725; PMID: 23329412
   PubMed Web of Science ®Google Scholar
• Morris HR, Waite AJ, Williams NM, Neal JW, Blake DJ. Recent advances in the genetics of the ALS-FTLD complex. Curr Neurol Neurosci Rep 2012; 12:243 - 50; http://dx.doi.org/10.1007/s11910-012-0268-5; PMID: 22477152
   PubMed Web of Science ®Google Scholar
• Kinch LN, Grishin NV. Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. Protein Sci 2006; 15:2669 - 74; http://dx.doi.org/10.1110/ps.062419006; PMID: 17075139
   PubMed Web of Science ®Google Scholar
• Nordmann M, Cabrera M, Perz A, Bröcker C, Ostrowicz C, Engelbrecht-Vandré S, et al. The Mon1-Ccz1 complex is the GEF of the late endosomal Rab7 homolog Ypt7. Curr Biol 2010; 20:1654 - 9; http://dx.doi.org/10.1016/j.cub.2010.08.002; PMID: 20797862
   PubMed Web of Science ®Google Scholar
• Carmona-Rivera C, Simeonov DR, Cardillo ND, Gahl WA, Cadilla CL. A divalent interaction between HPS1 and HPS4 is required for the formation of the biogenesis of lysosome-related organelle complex-3 (BLOC-3). Biochim Biophys Acta 2013; 1833:468 - 78; http://dx.doi.org/10.1016/j.bbamcr.2012.10.019; PMID: 23103514
   PubMed Web of Science ®Google Scholar
• Kowalczyk MS, Hughes JR, Babbs C, Sanchez-Pulido L, Szumska D, Sharpe JA, et al. Nprl3 is required for normal development of the cardiovascular system. Mamm Genome 2012; 23:404 - 15; http://dx.doi.org/10.1007/s00335-012-9398-y; PMID: 22538705
   PubMed Web of Science ®Google Scholar
• Neklesa TK, Davis RW. A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex. PLoS Genet 2009; 5:e1000515; http://dx.doi.org/10.1371/journal.pgen.1000515; PMID: 19521502
   PubMed Web of Science ®Google Scholar
• Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, et al. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics 2011; 10:M110 - , 006478; http://dx.doi.org/10.1074/mcp.M110.006478; PMID: 21454883
   PubMedGoogle Scholar
• Wu X, Tu BP. Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Mol Biol Cell 2011; 22:4124 - 33; http://dx.doi.org/10.1091/mbc.E11-06-0525; PMID: 21900499
   PubMed Web of Science ®Google Scholar
• Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM. Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 2010; 141:290 - 303; http://dx.doi.org/10.1016/j.cell.2010.02.024; PMID: 20381137
   PubMed Web of Science ®Google Scholar
• Bar-Peled L, Schweitzer LD, Zoncu R, Sabatini DM. Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1. Cell 2012; 150:1196 - 208; http://dx.doi.org/10.1016/j.cell.2012.07.032; PMID: 22980980
   PubMed Web of Science ®Google Scholar
• Kogan K, Spear ED, Kaiser CA, Fass D. Structural conservation of components in the amino acid sensing branch of the TOR pathway in yeast and mammals. J Mol Biol 2010; 402:388 - 98; http://dx.doi.org/10.1016/j.jmb.2010.07.034; PMID: 20655927
   PubMed Web of Science ®Google Scholar
• Wu B, Yee A, Ramelot T, Lemak A, Semesi A, Kennedy M, et al. Solution structure of hypothetical protein yst6499 from Saccharomyces cerevisiae. Northeast Structural Genomics Consortium Target YT727/ Ontario Center for Structural Proteomics Target yst6499; http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=2GRG.
   Google Scholar
• Hall J, Song Y, Karplus PA, Barbar E. The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. J Biol Chem 2010; 285:22566 - 75; http://dx.doi.org/10.1074/jbc.M110.103861; PMID: 20472935
   PubMed Web of Science ®Google Scholar
• Barrowman J, Bhandari D, Reinisch K, Ferro-Novick S. TRAPP complexes in membrane traffic: convergence through a common Rab. Nat Rev Mol Cell Biol 2010; 11:759 - 63; http://dx.doi.org/10.1038/nrm2999; PMID: 20966969
   PubMed Web of Science ®Google Scholar
• Scrivens PJ, Noueihed B, Shahrzad N, Hul S, Brunet S, Sacher M. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. Mol Biol Cell 2011; 22:2083 - 93; http://dx.doi.org/10.1091/mbc.E10-11-0873; PMID: 21525244
   PubMed Web of Science ®Google Scholar
• Koumandou VL, Dacks JB, Coulson RM, Field MC. Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins. BMC Evol Biol 2007; 7:29; http://dx.doi.org/10.1186/1471-2148-7-29; PMID: 17319956
   PubMed Web of Science ®Google Scholar
• Choi C, Davey M, Schluter C, Pandher P, Fang Y, Foster LJ, et al. Organization and assembly of the TRAPPII complex. Traffic 2011; 12:715 - 25; http://dx.doi.org/10.1111/j.1600-0854.2011.01181.x; PMID: 21453443
   PubMed Web of Science ®Google Scholar
• Kim YG, Raunser S, Munger C, Wagner J, Song YL, Cygler M, et al. The architecture of the multisubunit TRAPP I complex suggests a model for vesicle tethering. Cell 2006; 127:817 - 30; http://dx.doi.org/10.1016/j.cell.2006.09.029; PMID: 17110339
   PubMed Web of Science ®Google Scholar
• Jeyabalan J, Nesbit MA, Galvanovskis J, Callaghan R, Rorsman P, Thakker RV. SEDLIN forms homodimers: characterisation of SEDLIN mutations and their interactions with transcription factors MBP1, PITX1 and SF1. PLoS One 2010; 5:e10646; http://dx.doi.org/10.1371/journal.pone.0010646; PMID: 20498720
   PubMedGoogle Scholar
• Venditti R, Scanu T, Santoro M, Di Tullio G, Spaar A, Gaibisso R, et al. Sedlin controls the ER export of procollagen by regulating the Sar1 cycle. Science 2012; 337:1668 - 72; http://dx.doi.org/10.1126/science.1224947; PMID: 23019651
   PubMed Web of Science ®Google Scholar
• Zong M, Wu XG, Chan CW, Choi MY, Chan HC, Tanner JA, et al. The adaptor function of TRAPPC2 in mammalian TRAPPs explains TRAPPC2-associated SEDT and TRAPPC9-associated congenital intellectual disability. PLoS One 2011; 6:e23350; http://dx.doi.org/10.1371/journal.pone.0023350; PMID: 21858081
   PubMedGoogle Scholar
• Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol 2010; 17:1298 - 304; http://dx.doi.org/10.1038/nsmb.1914; PMID: 20972447
   PubMed Web of Science ®Google Scholar
• Jones S, Newman C, Liu F, Segev N. The TRAPP complex is a nucleotide exchanger for Ypt1 and Ypt31/32. Mol Biol Cell 2000; 11:4403 - 11; PMID: 11102533
   PubMed Web of Science ®Google Scholar
• Zou S, Liu Y, Zhang XQ, Chen Y, Ye M, Zhu X, et al. Modular TRAPP complexes regulate intracellular protein trafficking through multiple Ypt/Rab GTPases in Saccharomyces cerevisiae. Genetics 2012; 191:451 - 60; http://dx.doi.org/10.1534/genetics.112.139378; PMID: 22426882
   PubMed Web of Science ®Google Scholar
• Wang W, Sacher M, Ferro-Novick S. TRAPP stimulates guanine nucleotide exchange on Ypt1p. J Cell Biol 2000; 151:289 - 96; http://dx.doi.org/10.1083/jcb.151.2.289; PMID: 11038176
   PubMed Web of Science ®Google Scholar
• Chen S, Cai H, Park SK, Menon S, Jackson CL, Ferro-Novick S. Trs65p, a subunit of the Ypt1p GEF TRAPPII, interacts with the Arf1p exchange factor Gea2p to facilitate COPI-mediated vesicle traffic. Mol Biol Cell 2011; 22:3634 - 44; http://dx.doi.org/10.1091/mbc.E11-03-0197; PMID: 21813735
   PubMed Web of Science ®Google Scholar
• Fan S, Wei Z, Xu H, Gong W. Crystal structure of human synbindin reveals two conformations of longin domain. Biochem Biophys Res Commun 2009; 378:338 - 43; http://dx.doi.org/10.1016/j.bbrc.2008.04.143; PMID: 18466758
   PubMed Web of Science ®Google Scholar