1qze Citations

DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a.

Proc Natl Acad Sci U S A 100 12694-9 (2003)
Cited: 94 times
EuropePMC logo PMID: 14557549

Abstract

The Rad23 family of proteins, including the human homologs hHR23a and hHR23b, stimulates nucleotide excision repair and has been shown to provide a novel link between proteasome-mediated protein degradation and DNA repair. In this work, we illustrate how the proteasomal subunit S5a regulates hHR23a protein structure. By using NMR spectroscopy, we have elucidated the structure and dynamic properties of the 40-kDa hHR23a protein and show it to contain four structured domains connected by flexible linker regions. In addition, we reveal that these domains interact in an intramolecular fashion, and by using residual dipolar coupling data in combination with chemical shift perturbation analysis, we present the hHR23a structure. By itself, hHR23a adopts a closed conformation defined by the interaction of an N-terminal ubiquitin-like domain with two ubiquitin-associated domains. Interestingly, binding of the proteasomal subunit S5a disrupts the hHR23a interdomain interactions and thereby causes it to adopt an opened conformation.

Articles - 1qze mentioned but not cited (6)

  1. Structured States of Disordered Proteins from Genomic Sequences. Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Cell 167 158-170.e12 (2016)
  2. Modeling of molecular interaction between apoptin, BCR-Abl and CrkL--an alternative approach to conventional rational drug design. Panigrahi S, Stetefeld J, Jangamreddy JR, Mandal S, Mandal SK, Los M. PLoS One 7 e28395 (2012)
  3. Binding of HIV-1 Vpr protein to the human homolog of the yeast DNA repair protein RAD23 (hHR23A) requires its xeroderma pigmentosum complementation group C binding (XPCB) domain as well as the ubiquitin-associated 2 (UBA2) domain. Jung J, Byeon IJ, DeLucia M, Koharudin LM, Ahn J, Gronenborn AM. J Biol Chem 289 2577-2588 (2014)
  4. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
  5. Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations. Brown BP, Stein RA, Meiler J, Mchaourab HS. J Chem Theory Comput 20 1434-1447 (2024)
  6. research-article Approximating conformational Boltzmann distributions with AlphaFold2 predictions. Brown BP, Stein RA, Meiler J, Mchaourab H. bioRxiv 2023.08.06.552168 (2023)


Reviews citing this publication (25)

  1. Ubiquitin-binding domains. Hicke L, Schubert HL, Hill CP. Nat Rev Mol Cell Biol 6 610-621 (2005)
  2. Delivery of ubiquitinated substrates to protein-unfolding machines. Elsasser S, Finley D. Nat Cell Biol 7 742-749 (2005)
  3. Proteasome activators. Stadtmueller BM, Hill CP. Mol Cell 41 8-19 (2011)
  4. Regulated protein turnover: snapshots of the proteasome in action. Bhattacharyya S, Yu H, Mim C, Matouschek A. Nat Rev Mol Cell Biol 15 122-133 (2014)
  5. Integrating diverse data for structure determination of macromolecular assemblies. Alber F, Förster F, Korkin D, Topf M, Sali A. Annu Rev Biochem 77 443-477 (2008)
  6. Structural biology of the proteasome. Kish-Trier E, Hill CP. Annu Rev Biophys 42 29-49 (2013)
  7. Ubiquitin receptors and ERAD: a network of pathways to the proteasome. Raasi S, Wolf DH. Semin Cell Dev Biol 18 780-791 (2007)
  8. The diversity of ubiquitin recognition: hot spots and varied specificity. Winget JM, Mayor T. Mol Cell 38 627-635 (2010)
  9. Data-driven docking for the study of biomolecular complexes. van Dijk AD, Boelens R, Bonvin AM. FEBS J 272 293-312 (2005)
  10. Proteasome regulation of oxidative stress in aging and age-related diseases of the CNS. Ding Q, Dimayuga E, Keller JN. Antioxid Redox Signal 8 163-172 (2006)
  11. Disordered proteinaceous machines. Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek A, Lim RY, Xue B, Kurgan L, Uversky VN. Chem Rev 114 6806-6843 (2014)
  12. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. Skrisovska L, Schubert M, Allain FH. J Biomol NMR 46 51-65 (2010)
  13. Protein trans-splicing and its use in structural biology: opportunities and limitations. Volkmann G, Iwaï H. Mol Biosyst 6 2110-2121 (2010)
  14. The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy. Zientara-Rytter K, Subramani S. Cells 8 E40 (2019)
  15. Advances in integrative modeling of biomolecular complexes. Karaca E, Bonvin AM. Methods 59 372-381 (2013)
  16. Ubiquitin and its binding domains. Randles L, Walters KJ. Front Biosci (Landmark Ed) 17 2140-2157 (2012)
  17. Proteasomal recognition of ubiquitylated substrates. Fu H, Lin YL, Fatimababy AS. Trends Plant Sci 15 375-386 (2010)
  18. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. FEBS J 288 5231-5251 (2021)
  19. Ubiquitin-Modulated Phase Separation of Shuttle Proteins: Does Condensate Formation Promote Protein Degradation? Dao TP, Castañeda CA. Bioessays 42 e2000036 (2020)
  20. Structural disorder and its role in proteasomal degradation. Aufderheide A, Unverdorben P, Baumeister W, Förster F. FEBS Lett 589 2552-2560 (2015)
  21. Methods for the purification of ubiquitinated proteins. Tomlinson E, Palaniyappan N, Tooth D, Layfield R. Proteomics 7 1016-1022 (2007)
  22. Protein ligation: applications in NMR studies of proteins. Iwai H, Züger S. Biotechnol Genet Eng Rev 24 129-145 (2007)
  23. Proteasome substrate receptors and their therapeutic potential. Osei-Amponsa V, Walters KJ. Trends Biochem Sci 47 950-964 (2022)
  24. The role of ubiquitin-binding domains in human pathophysiology. Sokratous K, Hadjisavvas A, Diamandis EP, Kyriacou K. Crit Rev Clin Lab Sci 51 280-290 (2014)
  25. Every protagonist has a sidekick: Structural aspects of human xeroderma pigmentosum-binding proteins in nucleotide excision repair. Feltes BC. Protein Sci 30 2187-2205 (2021)

Articles citing this publication (63)

  1. Diverse polyubiquitin interaction properties of ubiquitin-associated domains. Raasi S, Varadan R, Fushman D, Pickart CM. Nat Struct Mol Biol 12 708-714 (2005)
  2. Proteasomes can degrade a significant proportion of cellular proteins independent of ubiquitination. Baugh JM, Viktorova EG, Pilipenko EV. J Mol Biol 386 814-827 (2009)
  3. Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. Wang Q, Young P, Walters KJ. J Mol Biol 348 727-739 (2005)
  4. Stress- and ubiquitylation-dependent phase separation of the proteasome. Yasuda S, Tsuchiya H, Kaiho A, Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernández-Busnadiego R, Tanaka K, Saeki Y. Nature 578 296-300 (2020)
  5. Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A. Raasi S, Orlov I, Fleming KG, Pickart CM. J Mol Biol 341 1367-1379 (2004)
  6. Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Ohno A, Jee J, Fujiwara K, Tenno T, Goda N, Tochio H, Kobayashi H, Hiroaki H, Shirakawa M. Structure 13 521-532 (2005)
  7. The Png1-Rad23 complex regulates glycoprotein turnover. Kim I, Ahn J, Liu C, Tanabe K, Apodaca J, Suzuki T, Rao H. J Cell Biol 172 211-219 (2006)
  8. Structural and functional analysis of ataxin-2 and ataxin-3. Albrecht M, Golatta M, Wüllner U, Lengauer T. Eur J Biochem 271 3155-3170 (2004)
  9. Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain. Trempe JF, Brown NR, Lowe ED, Gordon C, Campbell ID, Noble ME, Endicott JA. EMBO J 24 3178-3189 (2005)
  10. Rad23 escapes degradation because it lacks a proteasome initiation region. Fishbain S, Prakash S, Herrig A, Elsasser S, Matouschek A. Nat Commun 2 192 (2011)
  11. Rpn10-mediated degradation of ubiquitinated proteins is essential for mouse development. Hamazaki J, Sasaki K, Kawahara H, Hisanaga S, Tanaka K, Murata S. Mol Cell Biol 27 6629-6638 (2007)
  12. The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates. Martinez-Fonts K, Davis C, Tomita T, Elsasser S, Nager AR, Shi Y, Finley D, Matouschek A. Nat Commun 11 477 (2020)
  13. Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling. Long J, Garner TP, Pandya MJ, Craven CJ, Chen P, Shaw B, Williamson MP, Layfield R, Searle MS. J Mol Biol 396 178-194 (2010)
  14. Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome. Matiuhin Y, Kirkpatrick DS, Ziv I, Kim W, Dakshinamurthy A, Kleifeld O, Gygi SP, Reis N, Glickman MH. Mol Cell 32 415-425 (2008)
  15. UBL/UBA ubiquitin receptor proteins bind a common tetraubiquitin chain. Kang Y, Vossler RA, Diaz-Martinez LA, Winter NS, Clarke DJ, Walters KJ. J Mol Biol 356 1027-1035 (2006)
  16. Ddi1, a eukaryotic protein with the retroviral protease fold. Sirkis R, Gerst JE, Fass D. J Mol Biol 364 376-387 (2006)
  17. Loss of ubiquitin binding is a unifying mechanism by which mutations of SQSTM1 cause Paget's disease of bone. Cavey JR, Ralston SH, Sheppard PW, Ciani B, Gallagher TR, Long JE, Searle MS, Layfield R. Calcif Tissue Int 78 271-277 (2006)
  18. A puromycin-sensitive aminopeptidase is essential for meiosis in Arabidopsis thaliana. Sánchez-Morán E, Jones GH, Franklin FC, Santos JL. Plant Cell 16 2895-2909 (2004)
  19. Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ. Structure 24 1257-1270 (2016)
  20. Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12. Riedinger C, Boehringer J, Trempe JF, Lowe ED, Brown NR, Gehring K, Noble ME, Gordon C, Endicott JA. J Biol Chem 285 33992-34003 (2010)
  21. A conditional yeast E1 mutant blocks the ubiquitin-proteasome pathway and reveals a role for ubiquitin conjugates in targeting Rad23 to the proteasome. Ghaboosi N, Deshaies RJ. Mol Biol Cell 18 1953-1963 (2007)
  22. Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins. Lee JH, Choi JM, Lee C, Yi KJ, Cho Y. Proc Natl Acad Sci U S A 102 9144-9149 (2005)
  23. Structural insights into proteasome activation by the 19S regulatory particle. Ehlinger A, Walters KJ. Biochemistry 52 3618-3628 (2013)
  24. Yeast UBL-UBA proteins have partially redundant functions in cell cycle control. Díaz-Martínez LA, Kang Y, Walters KJ, Clarke DJ. Cell Div 1 28 (2006)
  25. High incidence of ubiquitin-like domains in human ubiquitin-specific proteases. Zhu X, Ménard R, Sulea T. Proteins 69 1-7 (2007)
  26. The STI and UBA Domains of UBQLN1 Are Critical Determinants of Substrate Interaction and Proteostasis. Kurlawala Z, Shah PP, Shah C, Beverly LJ. J Cell Biochem 118 2261-2270 (2017)
  27. Ubiquitin receptor proteins hHR23a and hPLIC2 interact. Kang Y, Zhang N, Koepp DM, Walters KJ. J Mol Biol 365 1093-1101 (2007)
  28. Defining how ubiquitin receptors hHR23a and S5a bind polyubiquitin. Kang Y, Chen X, Lary JW, Cole JL, Walters KJ. J Mol Biol 369 168-176 (2007)
  29. NMR-based model reveals the structural determinants of mammalian arylamine N-acetyltransferase substrate specificity. Zhang N, Liu L, Liu F, Wagner CR, Hanna PE, Walters KJ. J Mol Biol 363 188-200 (2006)
  30. Structure of hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle Factors and Substrates at the Proteasome. Chen X, Ebelle DL, Wright BJ, Sridharan V, Hooper E, Walters KJ. J Mol Biol 431 939-955 (2019)
  31. The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. Hänzelmann P, Stingele J, Hofmann K, Schindelin H, Raasi S. J Biol Chem 285 20390-20398 (2010)
  32. Rad23 interaction with the proteasome is regulated by phosphorylation of its ubiquitin-like (UbL) domain. Liang RY, Chen L, Ko BT, Shen YH, Li YT, Chen BR, Lin KT, Madura K, Chuang SM. J Mol Biol 426 4049-4060 (2014)
  33. Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction. Kamionka M, Feigon J. Protein Sci 13 2370-2377 (2004)
  34. Yeast Pth2 is a UBL domain-binding protein that participates in the ubiquitin-proteasome pathway. Ishii T, Funakoshi M, Kobayashi H. EMBO J 25 5492-5503 (2006)
  35. Defining an Embedded Code for Protein Ubiquitination. Jadhav T, Wooten MW. J Proteomics Bioinform 2 316 (2009)
  36. Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. Sirota FL, Ooi HS, Gattermayer T, Schneider G, Eisenhaber F, Maurer-Stroh S. BMC Genomics 11 Suppl 1 S15 (2010)
  37. Components of the ubiquitin-proteasome pathway compete for surfaces on Rad23 family proteins. Goh AM, Walters KJ, Elsasser S, Verma R, Deshaies RJ, Finley D, Howley PM. BMC Biochem 9 4 (2008)
  38. Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin. Zanzoni S, Ceccon A, Assfalg M, Singh RK, Fushman D, D'Onofrio M. Nanoscale 7 7197-7205 (2015)
  39. Rad4 regulates protein turnover at a postubiquitylation step. Li Y, Yan J, Kim I, Liu C, Huo K, Rao H. Mol Biol Cell 21 177-185 (2010)
  40. NMR characterization of the interaction between the PUB domain of peptide:N-glycanase and ubiquitin-like domain of HR23. Kamiya Y, Uekusa Y, Sumiyoshi A, Sasakawa H, Hirao T, Suzuki T, Kato K. FEBS Lett 586 1141-1146 (2012)
  41. Amino acid-selective segmental isotope labeling of multidomain proteins for structural biology. Michel E, Skrisovska L, Wüthrich K, Allain FH. Chembiochem 14 457-466 (2013)
  42. On the Mechanism of Hyperthermia-Induced BRCA2 Protein Degradation. van den Tempel N, Zelensky AN, Odijk H, Laffeber C, Schmidt CK, Brandsma I, Demmers J, Krawczyk PM, Kanaar R. Cancers (Basel) 11 E97 (2019)
  43. Solution structure and backbone dynamics of the XPC-binding domain of the human DNA repair protein hHR23B. Kim B, Ryu KS, Kim HJ, Cho SJ, Choi BS. FEBS J 272 2467-2476 (2005)
  44. The deubiquitylating enzyme Ubp12 regulates Rad23-dependent proteasomal degradation. Gödderz D, Giovannucci TA, Laláková J, Menéndez-Benito V, Dantuma NP. J Cell Sci 130 3336-3346 (2017)
  45. Identification of proteasome subunit beta type 6 (PSMB6) associated with deltamethrin resistance in mosquitoes by proteomic and bioassay analyses. Sun L, Ye Y, Sun H, Yu J, Zhang L, Sun Y, Zhang D, Ma L, Shen B, Zhu C. PLoS One 8 e65859 (2013)
  46. The SH3 domain of a M7 interacts with its C-terminal proline-rich region. Wang Q, Deloia MA, Kang Y, Litchke C, Zhang N, Titus MA, Walters KJ. Protein Sci 16 189-196 (2007)
  47. N-terminal deletion of peptide:N-glycanase results in enhanced deglycosylation activity. Wang S, Xin F, Liu X, Wang Y, An Z, Qi Q, Wang PG. PLoS One 4 e8335 (2009)
  48. Ion Mobility Mass Spectrometry Unveils Global Protein Conformations in Response to Conditions that Promote and Reverse Liquid-Liquid Phase Separation. Robb CG, Dao TP, Ujma J, Castañeda CA, Beveridge R. J Am Chem Soc 145 12541-12549 (2023)
  49. The ubiquitin-interacting motif of 26S proteasome subunit S5a induces A549 lung cancer cell death. Elangovan M, Choi ES, Jang BG, Kim MS, Yoo YJ. Biochem Biophys Res Commun 364 226-230 (2007)
  50. Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A. Byeon IL, Calero G, Wu Y, Byeon CH, Jung J, DeLucia M, Zhou X, Weiss S, Ahn J, Hao C, Skowronski J, Gronenborn AM. Nat Commun 12 6864 (2021)
  51. Letter Chemical shift assignments of the (poly)ubiquitin-binding region of the proteasome subunit S5a. Wang Q, Walters KJ. J Biomol NMR 30 231-232 (2004)
  52. Polyubiquitin and ubiquitin-like signals share common recognition sites on proteasomal subunit Rpn1. Boughton AJ, Zhang D, Singh RK, Fushman D. J Biol Chem 296 100450 (2021)
  53. Human Ubiquilin 2 and TDP-43 copathology drives neurodegeneration in transgenic Caenorhabditis elegans. Saxton AD, Kraemer BC. G3 (Bethesda) 11 jkab158 (2021)
  54. Identification of two isoforms of Dsk2-related protein XDRP1 in Xenopus eggs. Tanaka K, Funakoshi M, Inoue K, Kobayashi H. Biochem Biophys Res Commun 350 768-773 (2006)
  55. Insights into how protein dynamics affects arylamine N-acetyltransferase catalysis. Zhang N, Walters KJ. Biochem Biophys Res Commun 385 395-401 (2009)
  56. The Janus-faced E-values of HMMER2: extreme value distribution or logistic function? Wong WC, Maurer-Stroh S, Eisenhaber F. J Bioinform Comput Biol 9 179-206 (2011)
  57. The crystal structure of the ubiquitin-like (UbL) domain of human homologue A of Rad23 (hHR23A) protein. Chen YW, Tajima T, Agrawal S. Protein Eng Des Sel 24 131-138 (2011)
  58. A Cdc2-sensitive interaction of the UbL domain of XDRP1S with cyclin B mediates the degradation of cyclin B in Xenopus egg extracts. Tanaka K, Funakoshi M, Kobayashi H. Biochem Biophys Res Commun 350 774-782 (2006)
  59. A genetic screen in Drosophila reveals an unexpected role for the KIP1 ubiquitination-promoting complex in male fertility. Li W, Liang J, Outeda P, Turner S, Wakimoto BT, Watnick T. PLoS Genet 16 e1009217 (2020)
  60. Complete 1H, 13C, 15N resonance assignments and secondary structure of the Vpr binding region of hHR23A (residues 223-363). Byeon IL, Jung J, Byeon CH, DeLucia M, Ahn J, Gronenborn AM. Biomol NMR Assign 14 13-17 (2020)
  61. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Biochemistry 61 767-784 (2022)
  62. (1)H, (15)N, (13)C resonance assignments for Saccharomyces cerevisiae Rad23 UBL domain. Chen X, Walters KJ. Biomol NMR Assign 10 291-295 (2016)
  63. A Novel Interaction Between RAD23A/B and Y-family DNA Polymerases. Ashton NW, Jaiswal N, Moreno NC, Semenova IV, D'Orlando DA, Latancia MT, McIntyre J, Woodgate R, Bezsonova I. J Mol Biol 435 168353 (2023)