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Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins

Healy, Michael D., Sacharz, Joanna, McNally, Kerrie E., McConville, Calum, Tillu, Vikas A., Hall, Ryan J., Chilton, Molly, Cullen, Peter J., Mobli, Mehdi, Ghai, Rajesh, Stroud, David A., Collins, Brett M.·2022·Structure
DOI 10.1016/j.str.2022.10.001

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  • Our proteomic analyses routinely identified DENND10 as a Commander subunit.

    “As seen previously,6,16,20,21,22,68,69 our proteomic analyses routinely identified DENND10 as a Commander subunit (Figure S5C)”

    From Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome (2023) · cites this paper as [20]

    The Results (page unavailable) report that the proteomic experiment enriched known Retriever and CCC components, and the Figure 1 caption says it identified the entire Commander assembly. Our copy does not name DENND10 or establish that it was routinely identified, so those specifics cannot be verified from this source. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • The carboxy-terminal sequence of SNX17 is essential for binding to Commander.

    “The same sequence is essential for binding to Commander”

    From Mechanism and regulation of cargo entry into the Commander endosomal recycling pathway (2024) · cites this paper as [26]

  • A recent study showed that SNX17 CT could interact with the PDZ domain of a group of PDLIM proteins, which could provide a regulatory mechanism to decouple SNX17 and its cargoes from Retriever.

    “Finally, a recent study showed that SNX17 CT could interact with the PDZ domain of a group of PDLIM proteins, which could provide a regulatory mechanism to decouple SNX17 and its cargoes from Retriever43.”

    From Structural basis for Retriever-SNX17 assembly and endosomal sorting (2024) · cites this paper as [43]

  • The carboxy-terminal unstructured 465IGDEDL470 tail of SNX17, with Leu470 as the terminal residue, can bind directly to the PDZ domain of the PDLIM family of proteins.

    “Previously we showed that the carboxy-terminal unstructured 465IGDEDL470 tail of SNX17, Leu470 being the terminal residue, can bind directly to the PDZ domain of the PDLIM family of proteins26.”

    From Mechanism and regulation of cargo entry into the Commander endosomal recycling pathway (2024) · cites this paper as [26]

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Citations

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Research works printed but not linked: 68

  1. Bauer, 2000, Human CLP36, a PDZ-domain and LIM-domain protein, binds to alpha-actinin-1 and associates with actin filaments and stress fibers in activated platelets and endothelial cells, Blood, 96, 4236, 10.1182/blood.V96.13.4236 · DOI
  2. Böttcher, 2012, Sorting nexin 17 prevents lysosomal degradation of beta1 integrins by binding to the beta1-integrin tail, Nat. Cell Biol., 14, 584, 10.1038/ncb2501 · DOI · Paper page
  3. Camarata, 2006, LMP4 regulates Tbx5 protein subcellular localization and activity, J. Cell Biol., 174, 339, 10.1083/jcb.200511109 · DOI
  4. Campion, 2018, COMMD5/HCaRG hooks endosomes on cytoskeleton and coordinates EGFR trafficking, Cell Rep., 24, 670, 10.1016/j.celrep.2018.06.056 · DOI
  5. Chen, 2019, Towards a molecular understanding of endosomal trafficking by Retromer and Retriever, Traffic, 20, 465, 10.1111/tra.12649 · DOI · Paper page
  6. Clairfeuille, 2016, A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex, Nat. Struct. Mol. Biol., 23, 921, 10.1038/nsmb.3290 · DOI · Paper page
  7. Cox, 2008, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol., 26, 1367, 10.1038/nbt.1511 · DOI · Paper page
  8. D'Cruz, 2016, PDLIM7 is a novel target of the ubiquitin ligase Nedd4-1 in skeletal muscle, Biochem. J., 473, 267, 10.1042/BJ20150222 · DOI
  9. Dhanda, 2021, Distribution of PDLIM1 at actin-rich structures generated by invasive and adherent bacterial pathogens, Anat. Rec., 304, 919, 10.1002/ar.24523 · DOI
  10. Duleh, 2010, WASH and the Arp2/3 complex regulate endosome shape and trafficking, Cytoskeleton (Hoboken), 67, 193, 10.1002/cm.20437 · DOI · Paper page
  11. Elbediwy, 2018, Enigma proteins regulate YAP mechanotransduction, J. Cell Sci., 131, jcs221788, 10.1242/jcs.221788 · DOI
  12. Elkins, 2010, Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms, Protein Sci., 19, 731, 10.1002/pro.349 · DOI
  13. Ernst, 2014, A structural portrait of the PDZ domain family, J. Mol. Biol., 426, 3509, 10.1016/j.jmb.2014.08.012 · DOI
  14. Farfán, 2013, A sorting nexin 17-binding domain within the LRP1 cytoplasmic tail mediates receptor recycling through the basolateral sorting endosome, Traffic, 14, 823, 10.1111/tra.12076 · DOI · Paper page
  15. Faulkner, 1999, ZASP: a new Z-band alternatively spliced PDZ-motif protein, J. Cell Biol., 146, 465, 10.1083/jcb.146.2.465 · DOI
  16. Fu, 2010, Molecular determinants of PDLIM2 in suppressing HTLV-I Tax-mediated tumorigenesis, Oncogene, 29, 6499, 10.1038/onc.2010.374 · DOI
  17. Ghai, 2013, Structural basis for endosomal trafficking of diverse transmembrane cargos by PX-FERM proteins, Proc. Natl. Acad. Sci. USA, 110, E643, 10.1073/pnas.1216229110 · DOI · Paper page
  18. Ghai, 2011, Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases, Proc. Natl. Acad. Sci. USA, 108, 7763, 10.1073/pnas.1017110108 · DOI · Paper page
  19. Gomez, 2012, Trafficking defects in WASH-knockout fibroblasts originate from collapsed endosomal and lysosomal networks, Mol. Biol. Cell, 23, 3215, 10.1091/mbc.e12-02-0101 · DOI · Paper page
  20. Güntert, 2015, Combined automated NOE assignment and structure calculation with CYANA, J. Biomol. NMR, 62, 453, 10.1007/s10858-015-9924-9 · DOI
  21. Hasegawa, 2010, CLP36 interacts with palladin in dorsal root ganglion neurons, Neurosci. Lett., 476, 53, 10.1016/j.neulet.2010.03.081 · DOI
  22. Hock, 2020, HIGD2A is required for assembly of the COX3 module of human mitochondrial complex IV, Mol. Cell. Proteomics, 19, 1145, 10.1074/mcp.RA120.002076 · DOI
  23. Huang, 2020, An overview of the cytoskeleton-associated role of PDLIM5, Front. Physiol., 11, 975, 10.3389/fphys.2020.00975 · DOI
  24. Katzemich, 2013, Alp/Enigma family proteins cooperate in Z-disc formation and myofibril assembly, PLoS Genet., 9, e1003342, 10.1371/journal.pgen.1003342 · DOI
  25. Klaavuniemi, 2009, Characterization of the interaction between Actinin-Associated LIM Protein (ALP) and the rod domain of alpha-actinin, BMC Cell Biol., 10, 22, 10.1186/1471-2121-10-22 · DOI
  26. Klaavuniemi, 2004, The ZASP-like motif in actinin-associated LIM protein is required for interaction with the alpha-actinin rod and for targeting to the muscle Z-line, J. Biol. Chem., 279, 26402, 10.1074/jbc.M401871200 · DOI
  27. Klein, 2018, PDLIM7 and CDH18 regulate the turnover of MDM2 during CDK4/6 inhibitor therapy-induced senescence, Oncogene, 37, 5066, 10.1038/s41388-018-0332-y · DOI
  28. Krause, 2004, Tbx5 and Tbx4 transcription factors interact with a new chicken PDZ-LIM protein in limb and heart development, Dev. Biol., 273, 106, 10.1016/j.ydbio.2004.05.024 · DOI
  29. Krcmery, 2010, Nucleocytoplasmic functions of the PDZ-LIM protein family: new insights into organ development, Bioessays, 32, 100, 10.1002/bies.200900148 · DOI
  30. Lee, 2010, PDZ domains and their binding partners: structure, specificity, and modification, Cell Commun. Signal., 8, 8, 10.1186/1478-811X-8-8 · DOI
  31. Li, 2015, Endosomal sorting of Notch receptors through COMMD9-dependent pathways modulates Notch signaling, J. Cell Biol., 211, 605, 10.1083/jcb.201505108 · DOI · Paper page
  32. Liu, 2015, PDZ and LIM domain protein 1(PDLIM1)/CLP36 promotes breast cancer cell migration, invasion and metastasis through interaction with alpha-actinin, Oncogene, 34, 1300, 10.1038/onc.2014.64 · DOI
  33. Long, 2005, Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem, Nat. Struct. Mol. Biol., 12, 722, 10.1038/nsmb958 · DOI
  34. Mallam, 2017, Systems-wide studies uncover commander, a multiprotein complex essential to human development, Cell Syst., 4, 483, 10.1016/j.cels.2017.04.006 · DOI · Paper page
  35. Marley, 2001, A method for efficient isotopic labeling of recombinant proteins, J. Biomol. NMR, 20, 71, 10.1023/A:1011254402785 · DOI
  36. Nomme, 2015, Structural basis of a key factor regulating the affinity between the zonula occludens first PDZ domain and claudins, J. Biol. Chem., 290, 16595, 10.1074/jbc.M115.646695 · DOI
  37. Passier, 2000, Oracle, a novel PDZ-LIM domain protein expressed in heart and skeletal muscle, Mech. Dev., 92, 277, 10.1016/S0925-4773(99)00330-5 · DOI
  38. Perez-Riverol, 2019, The PRIDE database and related tools and resources in 2019: improving support for quantification data, Nucleic Acids Res., 47, D442, 10.1093/nar/gky1106 · DOI
  39. Phillips-Krawczak, 2015, COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A, Mol. Biol. Cell, 26, 91, 10.1091/mbc.e14-06-1073 · DOI · Paper page
  40. Pomiès, 1999, Purification and characterization of an alpha-actinin-binding PDZ-LIM protein that is up-regulated during muscle differentiation, J. Biol. Chem., 274, 29242, 10.1074/jbc.274.41.29242 · DOI
  41. Schulz, 2004, Actin/alpha-actinin-dependent transport of AMPA receptors in dendritic spines: role of the PDZ-LIM protein RIL, J. Neurosci., 24, 8584, 10.1523/JNEUROSCI.2100-04.2004 · DOI
  42. Shen, 2015, Protein structural information derived from NMR chemical shift with the neural network program TALOS-N, Methods Mol. Biol., 1260, 17, 10.1007/978-1-4939-2239-0_2 · DOI
  43. Shi, 2020, PDLIM5 inhibits STUB1-mediated degradation of SMAD3 and promotes the migration and invasion of lung cancer cells, J. Biol. Chem., 295, 13798, 10.1074/jbc.RA120.014976 · DOI
  44. Simonetti, 2019, Actin-dependent endosomal receptor recycling, Curr. Opin. Cell Biol., 56, 22, 10.1016/j.ceb.2018.08.006 · DOI · Paper page
  45. Skinner, 2016, CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis, J. Biomol. NMR, 66, 111, 10.1007/s10858-016-0060-y · DOI
  46. Starokadomskyy, 2013, CCDC22 deficiency in humans blunts activation of proinflammatory NF-kappa B signaling, J. Clin. Invest., 123, 2244, 10.1172/JCI66466 · DOI · Paper page
  47. Steinberg, 2012, SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways, J. Cell Biol., 197, 219, 10.1083/jcb.201111121 · DOI · Paper page
  48. Subbaiah, 2011, PDZ domains: the building blocks regulating tumorigenesis, Biochem. J., 439, 195, 10.1042/BJ20110903 · DOI
  49. Sugi, 2007, Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation, EMBO J., 26, 2192, 10.1038/sj.emboj.7601651 · DOI
  50. Tamura, 2007, The PDZ-LIM protein CLP36 is required for actin stress fiber formation and focal adhesion assembly in BeWo cells, Sci. World J., 364, 589
  51. te Velthuis, 2007, PDZ and LIM domain-encoding genes: molecular interactions and their role in development, Sci. World J., 7, 1470, 10.1100/tsw.2007.232 · DOI
  52. Tseng, 2014, Sorting nexin 31 binds multiple beta integrin cytoplasmic domains and regulates beta1 integrin surface levels and stability, J. Mol. Biol., 426, 3180, 10.1016/j.jmb.2014.07.003 · DOI
  53. Tyanova, 2016, The Perseus computational platform for comprehensive analysis of (prote)omics data, Nat. Methods, 13, 731, 10.1038/nmeth.3901 · DOI · Paper page
  54. Urban, 2016, Pdlim7 regulates arf6-dependent actin dynamics and is required for platelet-mediated thrombosis in mice, PLoS One, 11, e0164042, 10.1371/journal.pone.0164042 · DOI
  55. Vallenius, 2000, CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4, J. Biol. Chem., 275, 11100, 10.1074/jbc.275.15.11100 · DOI
  56. Vallenius, 2004, The PDZ-LIM protein RIL modulates actin stress fiber turnover and enhances the association of alpha-actinin with F-actin, Exp. Cell Res., 293, 117, 10.1016/j.yexcr.2003.09.004 · DOI
  57. Vieira, 2014, SNX31: a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells, PLoS One, 9, e99644, 10.1371/journal.pone.0099644 · DOI
  58. von Nandelstadh, 2009, A class III PDZ binding motif in the myotilin and FATZ families binds enigma family proteins: a common link for Z-disc myopathies, Mol. Cell Biol., 29, 822, 10.1128/MCB.01454-08 · DOI
  59. Wan, 2015, Panorama of ancient metazoan macromolecular complexes, Nature, 525, 339, 10.1038/nature14877 · DOI
  60. Weeratunga, 2020, Recognising the signals of endosomal trafficking, Curr. Opin. Cell Biol., 65, 17, 10.1016/j.ceb.2020.02.005 · DOI · Paper page
  61. Wu, 2016, BioGPS: building your own mash-up of gene annotations and expression profiles, Nucleic Acids Res., 44, D313, 10.1093/nar/gkv1104 · DOI
  62. Xia, 1997, Actinin-associated LIM protein: identification of a domain interaction between PDZ and spectrin-like repeat motifs, J. Cell Biol., 139, 507, 10.1083/jcb.139.2.507 · DOI
  63. Yan, 2009, PDLIM2 suppresses human T-cell leukemia virus type I Tax-mediated tumorigenesis by targeting Tax into the nuclear matrix for proteasomal degradation, Blood, 113, 4370, 10.1182/blood-2008-10-185660 · DOI
  64. Ye, 2013, Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures, Biochem. J., 455, 1, 10.1042/BJ20130783 · DOI
  65. Yi, 2014, Systematic analysis of bacterial effector-postsynaptic density 95/disc large/zonula occludens-1 (PDZ) domain interactions demonstrates Shigella OspE protein promotes protein kinase C activation via PDLIM proteins, J. Biol. Chem., 289, 30101, 10.1074/jbc.M114.595868 · DOI
  66. Yu, 2011, PDlim2 selectively interacts with the PDZ binding motif of highly pathogenic avian H5N1 influenza A virus NS1, PLoS One, 6, e19511, 10.1371/journal.pone.0019511 · DOI
  67. Zheng, 2010, ALP/Enigma PDZ-LIM domain proteins in the heart, J. Mol. Cell Biol., 2, 96, 10.1093/jmcb/mjp038 · DOI · Paper page
  68. Zhou, 1999, Cypher, a striated muscle-restricted PDZ and LIM domain-containing protein, binds to alpha-actinin-2 and protein kinase C, J. Biol. Chem., 274, 19807, 10.1074/jbc.274.28.19807 · DOI

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Metadata

Authors
Healy, M. D., Sacharz, J., McNally, K. E., McConville, C., Tillu, V. A., Hall, R. J., Chilton, M., Cullen, P. J., Mobli, M., Ghai, R., Stroud, D. A., & Collins, B. M.
Venue
Structure
Publisher
Elsevier BV
Published
2022-12
Volume
30
Issue
12
Pages
1590-1602.e6
ISSN
0969-2126
DOI
10.1016/j.str.2022.10.001
Cited by
23
References
9
Language
en
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