Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein
Open accessAbstract
The folliculin/Fnip complex has been demonstrated to play a crucial role in the mechanisms underlying Birt–Hogg–Dubé (BHD) syndrome, a rare inherited cancer syndrome. Lst4 has been previously proposed to be the Fnip1/2 orthologue in yeast and therefore a member of the DENN family. In order to confirm this, we solved the crystal structure of the N-terminal region of Lst4 from Kluyveromyces lactis and show it contains a longin domain, the first domain of the full DENN module. Furthermore, we demonstrate that Lst4 through its DENN domain interacts with Lst7, the yeast folliculin orthologue. Like its human counterpart, the Lst7/Lst4 complex relocates to the vacuolar membrane in response to nutrient starvation, most notably in carbon starvation. Finally, we express and purify the recombinant Lst7/Lst4 complex and show that it exists as a 1 : 1 heterodimer in solution. This work confirms the membership of Lst4 and the Fnip proteins in the DENN family, and provides a basis for using the Lst7/Lst4 complex to understand the molecular function of folliculin and its role in the pathogenesis of BHD syndrome.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The structure of the Kluyveromyces lactis Lst4 N-terminal longin domain revealed a classic longin domain architecture, the first subdomain of the complete DENN.
“The structure revealed a classic longin domain architecture, which is the first subdomain of the complete DENN”
From Signal integration in the (m)TORC1 growth pathway (2018) · cites this paper as Pacitto et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463 · see citing works
Solvent content of protein crystals
Matthews, B. W. (1968) · Journal of Molecular Biology · doi:10.1016/0022-2836(68)90205-2 · Cited by 7,970 · see citing works
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkòczi, G., Chen, V. B., Davis, I., Echols, N., Headd, J. J., Hung, L., Kapral, G. J., Grosse‐Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334 · see citing works
How good are my data and what is the resolution?
Evans, P. R., & Murshudov, G. N. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913000061 · Cited by 4,747 · see citing works
Schuck, P. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76713-0 · Cited by 3,868 · see citing works
Dali server: conservation mapping in 3D
Holm, L., & Rosenstr�m, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq366 · Cited by 3,640 · see citing works
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works
Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben‐Tal, N. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq399 · Cited by 1,822 · see citing works
The Yeast Nuclear Pore Complex
Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., & Chait, B. T. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.148.4.635 · Cited by 1,403 · see citing works
Barlowe, C. K. (1994) · Cell · doi:10.1016/0092-8674(94)90138-4 · Cited by 1,329 · see citing works
Nickerson, M. L., Warren, M. B., Toro, J. R., Matrosova, V. Y., Glenn, G. M., Turner, M. L. C., Duray, P. H., Merino, M. J., Choyke, P. L., Pavlovich, C. P., et al. (2002) · Cancer Cell · doi:10.1016/s1535-6108(02)00104-6 · Cited by 932 · see citing works
Martina, J. A., Diab, H. I., Lishu, L., Jeong-A, L., Patange, S., Raben, N., & Puertollano, R. (2014) · Science Signaling · doi:10.1126/scisignal.2004754 · Cited by 677 · see citing works
Birt-Hogg-Dubé syndrome: diagnosis and management
Menko, F. H., Steensel, M. A. M. V., Giraud, S., Friis-Hansen, L. J., Richard, S., Ungari, S., Nordenskjöld, M., Hansen, T. V. O., Solly, J., & Maher, E. R. (2009) · The Lancet Oncology · doi:10.1016/s1470-2045(09)70188-3 · Cited by 592 · see citing works
Tsun, Z.-Y., Bar-Peled, L., Chantranupong, L., Zoncu, R., Wang, T., Kim, C., Spooner, E., & Sabatini, D. M. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.09.016 · Cited by 565 · see citing works
Determining the architectures of macromolecular assemblies
Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D. P., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B. T., et al. (2007) · Nature · doi:10.1038/nature06404 · Cited by 525 · see citing works
Self-citationDefinition of general topological equivalence in protein structures
Šali, A., & Blundell, T. L. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90134-8 · Cited by 501 · see citing works
Self-citationBaba, M., Hong, S., Sharma, N. D., Warren, M. B., Nickerson, M. L., Iwamatsu, A., Esposito, D., Gillette, W., Hopkins, R. F., Hartley, J. L., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603781103 · Cited by 491 · see citing works
Recruitment of folliculin to lysosomes supports the amino acid–dependent activation of Rag GTPases
Petit, C. S., Roczniak-Ferguson, A., & Ferguson, S. M. (2013) · Journal of Cell Biology · doi:10.1083/jcb.201307084 · Cited by 355 · see citing works
Siniossoglou, S., Wimmer, C., Rieger, M. A., Doye, V., Tekotte, H., Weise, C., Emig, S., Segref, A., & Hurt, E. C. (1996) · Cell · doi:10.1016/s0092-8674(00)80981-2 · Cited by 321 · see citing works
Levine, T. P., Daniels, R. D., Gatta, A. T., Wong, L. H., & Hayes, M. J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts725 · Cited by 321 · see citing works
Self-citationRab GTPase regulation of membrane identity
Pfeffer, S. R. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.04.002 · Cited by 319 · see citing works
T7 Vectors with a Modified T7lacPromoter for Expression of Proteins inEscherichia coli
Peränen, J., Rikkonen, M., Hyvönen, M., & Kääriäinen, L. (1996) · Analytical Biochemistry · doi:10.1006/abio.1996.0187 · Cited by 270 · see citing works
DENN Domain Proteins: Regulators of Rab GTPases
Marat, A. L., Dokainish, H., & McPherson, P. S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.r110.217067 · Cited by 265 · see citing works
Zhang, D., Iyer, L. M., He, F., & Aravind, L. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00283 · Cited by 244 · see citing works
The role of the Birt–Hogg–Dubé protein in mTOR activation and renal tumorigenesis
Hartman, T. R., Nicolas, É., Klein–Szanto, A. J., Al‐Saleem, T., Cash, T. P., Simon, M. C., & Henske, E. P. (2009) · Oncogene · doi:10.1038/onc.2009.14 · Cited by 215 · see citing works
Identification and characterization of a novel folliculin-interacting protein FNIP2
Hasumi, H., Baba, M., Hong, S., Hasumi, Y., Huang, Y. K., Yao, M., Valera, V., Linehan, W. M., & Schmidt, L. S. (2008) · Gene · doi:10.1016/j.gene.2008.02.022 · Cited by 191 · see citing works
Péli-Gulli, M.-P., Sardu, A., Panchaud, N., Raucci, S., & De Virgilio, C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.08.059 · Cited by 157 · see citing works
Roberg, K. J., Bickel, S. E., Rowley, N., & Kaiser, C. A. (1997) · Genetics · doi:10.1093/genetics/147.4.1569 · Cited by 146 · see citing works
Dokudovskaya, S., Waharte, F., Schlessinger, A., Pieper, U., Devos, D. P., Cristea, I. M., Williams, R., Salamero, J., Chait, B. T., Šali, A., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.006478 · Cited by 145 · see citing works
Self-citationTakagi, Y., Kobayashi, T., Shiono, M., Wang, L., Piao, X., Sun, G., Zhang, D., Abe, M., Hagiwara, Y., Takahashi, K., et al. (2008) · Oncogene · doi:10.1038/onc.2008.261 · Cited by 135 · see citing works
The tumor suppressor folliculin regulates AMPK-dependent metabolic transformation
Yan, M., Gingras, M., Dunlop, E. A., Nouët, Y., Dupuy, F., Jalali, Z., Possik, E., Coull, B. J., Kharitidi, D., Dydensborg, A. B., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci71749 · Cited by 134 · see citing works
Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA
Ascher, D. B., Wielens, J., Nero, T. L., Doughty, L., Morton, C. J., & Parker, M. W. (2014) · Scientific Reports · doi:10.1038/srep04765 · Cited by 116 · see citing works
Self-citationWu, X., Bradley, M. J., Cai, Y., Kümmel, D., Cruz, E. M. D. L., Barr, F. A., & Reinisch, K. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110415108 · Cited by 111 · see citing works
Folliculin Regulates Ampk-Dependent Autophagy and Metabolic Stress Survival
Possik, E., Jalali, Z., Nouët, Y., Yan, M., Gingras, M., Schmeißer, K., Panaite, L., Dupuy, F., Kharitidi, D., Chotard, L., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004273 · Cited by 111 · see citing works
Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer
Nookala, R. K., Langemeyer, L., Pacitto, A., Ochoa-Montaño, B., Donaldson, J. C., Blaszczyk, B. K., Chirgadze, D. Y., Barr, F. A., Bazan, J. F., & Blundell, T. L. (2012) · Open Biology · doi:10.1098/rsob.120071 · Cited by 106 · see citing works
Self-citationLevine, T. P., Daniels, R. D., Wong, L. H., Gatta, A. T., Gerondopoulos, A., & Barr, F. A. (2013) · Small GTPases · doi:10.4161/sgtp.24262 · Cited by 93 · cited 1× · see citing works
“While the core members are reasonably well conserved at the sequence level, the wider family is much more divergent and could only be detected by a more sensitive fold-recognition approach [18,19].”
BackgroundSelf-citationBirt–Hogg–Dubé syndrome is a novel ciliopathy
Luijten, M., Basten, S. G., Claessens, T., Vernooij, M., Scott, C. L., Janssen, R., Easton, J. A., Kamps, M. A. F., Vreeburg, M., Broers, J. L. V., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt288 · Cited by 85 · see citing works
Self-citationvan Slegtenhorst, M., Khabibullin, D., Hartman, T. R., Nicolas, É., Kruger, W. D., & Henske, E. P. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700857200 · Cited by 81 · see citing works
FLCN, a novel autophagy component, interacts with GABARAP and is regulated by ULK1 phosphorylation
Dunlop, E. A., Seifan, S., Claessens, T., Behrends, C., Kamps, M. A. F., Rozycka, E., Kemp, A. J., Nookala, R. K., Blenis, J., Coull, B. J., et al. (2014) · Autophagy · doi:10.4161/auto.29640 · Cited by 80 · see citing works
Self-citationCrystal structure of human insulin‐regulated aminopeptidase with specificity for cyclic peptides
Hermans, S. J., Ascher, D. B., Hancock, N. C., Holien, J. K., Michell, B. J., Chai, S. Y., Morton, C. J., & Parker, M. W. (2014) · Protein Science · doi:10.1002/pro.2604 · Cited by 67 · see citing works
Self-citationCash, T. P., Gruber, J. J., Hartman, T. R., Henske, E. P., & Simon, M. C. (2011) · Oncogene · doi:10.1038/onc.2010.628 · Cited by 59 · see citing works
Schlenker, O., Hendricks, A., Sinning, I., & Wild, K. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512415200 · Cited by 49 · see citing works
Longin and GAF Domains: Structural Evolution and Adaptation to the Subcellular Trafficking Machinery
Franceschi, N. D., Wild, K., Schlacht, A., Dacks, J. B., Sinning, I., & Filippini, F. (2013) · Traffic · doi:10.1111/tra.12124 · Cited by 46 · see citing works
Wishart, J. A., Osborn, M. J., Gent, M. E., Yen, K., Vujovic, Z., Gitsham, P., Zhang, N., Miller, J., & Oliver, S. G. (2006) · Yeast · doi:10.1002/yea.1348 · Cited by 16 · see citing works
Self-citationCrystal structure of human synbindin reveals two conformations of longin domain
Fan, S., Wei, Z., Xu, H., & Gong, W. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.04.143 · Cited by 11 · see citing works
Crystal structure of the yeast TRAPP ‐associated protein Tca17
Wang, C., Gohlke, U., Roske, Y., et al. (2014) · FEBS Journal · doi:10.1111/febs.12888 · Cited by 11 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Starling, G. P., Yip, Y. Y., Sanger, A., Morton, P. E., Eden, E. R., & Dodding, M. P. (2016) · The EMBO Reports · doi:10.15252/embr.201541382 · Cited by 96 · see citing works
Péli-Gulli, M.-P., Raucci, S., Hu, Z., Dengjel, J., & De Virgilio, C. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.058 · Cited by 28 · see citing works
Signal integration in the (m)TORC1 growth pathway
Ramlaul, K., & Aylett, C. H. S. (2018) · Frontiers in Biology · doi:10.1007/s11515-018-1501-7 · Cited by 12 · see citing works
Folliculin – A tumor suppressor at the intersection of metabolic signaling and membrane traffic
Dodding, M. P. (2017) · Small GTPases · doi:10.1080/21541248.2016.1204808 · Cited by 8 · see citing works
- Authors
- Pacitto, A., Ascher, D. B., Wong, L. H., Blaszczyk, B. K., Nookala, R. K., Zhang, N., Dokudovskaya, S., Levine, T. P., & Blundell, T. L.
- Affiliations
- University of Cambridge (GB)
- University College London (GB)
- Université Paris-Sud (FR)
- Corresponding author
- Pacitto, Angela
- Blundell, Tom L.
- ORCID
- Venue
- Open Biology
- Publisher
- The Royal Society
- Published
- 2015-12
- Volume
- 5
- Issue
- 12
- Pages
- 150174
- ISSN
- 2046-2441 (ISSN-L)
- PMC
- PMC4703059
- OpenAlex
- W2213367053
- Cited by
- 28
- References
- 48
- Citations by year
- 2025: 2 · 2024: 1 · 2023: 1 · 2021: 4 · 2020: 3 · 2019: 6 · 2018: 3 · 2017: 4 · 2016: 4
- FWCI
- 1.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Open Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Funders
- Wellcome Trust
- Myrovlytis Trust
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Keywords
- folliculin, Birt-Hogg-Dubé syndrome, longin domain, Kluyveromyces lactis, heterodimer, tonoplast, carbon starvation, nutrient deprivation, crystal structure
- MeSH terms
- Fungal Proteins, Kluyveromyces, Protein Structure, Secondary, Protein Structure, Tertiary, Saccharomyces cerevisiae Proteins, Vesicular Transport Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review