#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease


Herpesviruses encode a unique serine protease, which is essential for herpesvirus capsid maturation and is therefore an interesting target for drug development. In solution, this protease exists in an equilibrium of an inactive monomeric and an active dimeric form. All currently available crystal structures of herpesvirus proteases represent complexes, particularly dimers. Here we show the first three-dimensional structure of the native monomeric form in addition to the native and the chemically inactivated dimeric form of the protease derived from the porcine herpesvirus pseudorabies virus. Comparison of the monomeric and dimeric form allows predictions on the structural changes that occur during dimerization and shed light onto the process of protease activation. These new crystal structures provide a rational base to develop drugs preventing dimerization and therefore impeding herpesvirus capsid maturation. Furthermore, it is likely that this mechanism is conserved throughout the herpesviruses.


Vyšlo v časopise: Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease. PLoS Pathog 11(7): e32767. doi:10.1371/journal.ppat.1005045
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1005045

Souhrn

Herpesviruses encode a unique serine protease, which is essential for herpesvirus capsid maturation and is therefore an interesting target for drug development. In solution, this protease exists in an equilibrium of an inactive monomeric and an active dimeric form. All currently available crystal structures of herpesvirus proteases represent complexes, particularly dimers. Here we show the first three-dimensional structure of the native monomeric form in addition to the native and the chemically inactivated dimeric form of the protease derived from the porcine herpesvirus pseudorabies virus. Comparison of the monomeric and dimeric form allows predictions on the structural changes that occur during dimerization and shed light onto the process of protease activation. These new crystal structures provide a rational base to develop drugs preventing dimerization and therefore impeding herpesvirus capsid maturation. Furthermore, it is likely that this mechanism is conserved throughout the herpesviruses.


Zdroje

1. Card JP, Rinaman L, Schwaber JS, Miselis RR, Whealy ME, Robbins AK, et al. (1990) Neurotropic properties of pseudorabies virus: uptake and transneuronal passage in the rat central nervous system. J Neurosci 10: 1974–1994. 2162388

2. Ben-Porat T, Veach RA, Ihara S (1983) Localization of the regions of homology between the genomes of herpes simplex virus, type 1, and pseudorabies virus. Virology 127: 194–204. 6305015

3. Klupp BG, Hengartner CJ, Mettenleiter TC, Enquist LW (2004) Complete, annotated sequence of the pseudorabies virus genome. J Virol 78: 424–440. 14671123

4. Preston VG, Coates JA, Rixon FJ (1983) Identification and characterization of a herpes simplex virus gene product required for encapsidation of virus DNA. J Virol 45: 1056–1064. 6300447

5. Liu FY, Roizman B (1991) The herpes simplex virus 1 gene encoding a protease also contains within its coding domain the gene encoding the more abundant substrate. J Virol 65: 5149–5156. 1654435

6. Liu FY, Roizman B (1991) The promoter, transcriptional unit, and coding sequence of herpes simplex virus 1 family 35 proteins are contained within and in frame with the UL26 open reading frame. J Virol 65: 206–212. 1845885

7. Welch AR, McNally LM, Gibson W (1991) Cytomegalovirus assembly protein nested gene family: four 3'-coterminal transcripts encode four in-frame, overlapping proteins. J Virol 65: 4091–4100. 1649317

8. Welch AR, Woods AS, McNally LM, Cotter RJ, Gibson W (1991) A herpesvirus maturational proteinase, assemblin: identification of its gene, putative active site domain, and cleavage site. Proc Natl Acad Sci USA 88: 10792–10796. 1961747

9. Stevens JT, Mapelli C, Tsao J, Hail M, O'Boyle II D, et al. (1994) In vitro proteolytic activity and active-site identification of the human cytomegalovirus protease. Eur J Biochem 226: 361–367. 8001553

10. DiIanni CL, Drier DA, Deckman IC, McCann PJ, Liu FY, et al. (1993) Identification of the herpes simplex virus-1 protease cleavage sites by direct sequence analysis of autoproteolytic cleavage products. J Biol Chem 268: 2048–2051. 8380586

11. Beaudet-Miller M, Zhang R, Durkin J, Gibson W, Kwong AD, et al. (1996) Virus-specific interaction between the human cytomegalovirus major capsid protein and the C terminus of the assembly protein precursor. J Virol 70: 8081–8088. 8892933

12. Desai P, Person S (1996) Molecular Interactions between the HSV-1 Capsid Proteins as Measured by the Yeast Two-Hybrid System. Virology 220: 516–521. 8661404

13. Hong Z, Beaudet-Miller M, Durkin J, Zhang R, Kwong AD (1996) Identification of a minimal hydrophobic domain in the herpes simplex virus type 1 scaffolding protein which is required for interaction with the major capsid protein. J Virol 70: 533–540. 8523566

14. Nicholson P, Addison C, Cross A, Kennard J, Preston VG, et al. (1994) Localization of the herpes simplex virus type 1 major capsid protein VP5 to the cell nucleus requires the abundant scaffolding protein VP22a. J Gen Virol 75: 1091–1099. 8176370

15. Pelletier A, Dô F, Brisebois JJ, Lagacé L, Cordingley MG (1997) Self-association of herpes simplex virus type 1 ICP35 is via coiled-coil interactions and promotes stable interaction with the major capsid protein. J Virol 71: 5197–5208. 9188587

16. Thomsen DR, Newcomb WW, Brown JC, Homa FL (1995) Assembly of the herpes simplex virus capsid: requirement for the carboxyl-terminal twenty-five amino acids of the proteins encoded by the UL26 and UL26. 5 genes. J Virol 69: 3690–3703. 7745718

17. Wood LJ, Baxter MK, Plafker SM, Gibson W (1997) Human cytomegalovirus capsid assembly protein precursor (pUL80.5) interacts with itself and with the major capsid protein (pUL86) through two different domains. J Virol 71: 179–190. 8985337

18. Sheaffer AK, Newcomb WW, Brown JC, Gao M, Weller SK, Tenney DJ (2000) Evidence for controlled incorporation of herpes simplex virus type 1 UL26 protease into capsids. J Virol 74: 6838–6848. 10888623

19. Church GA, Wilson DW (1997) Study of herpes simplex virus maturation during a synchronous wave of assembly. J Virol 71: 3603–3612. 9094633

20. Dezélée S, Bras F, Vende P, Simonet B, Nguyen X, et al. (1996) The BamHI fragment 9 of pseudorabies virus contains genes homologous to the UL24, UL25, UL26, and UL 26.5 genes of herpes simplex virus type 1. Virus Res 42: 27–39. 8806172

21. Gibson W, Welch AR, Hall MRT (1994) Assemblin, a herpes virus serine maturational proteinase and new molecular target for antivirals. Perspect Drug Discov 2: 413–426.

22. Thomsen DR, Roof LL, Homa FL (1994) Assembly of herpes simplex virus (HSV) intermediate capsids in insect cells infected with recombinant baculoviruses expressing HSV capsid proteins. J Virol 68: 2442–2457. 8139029

23. Pray TR, Nomura AM, Pennington MW, Craik CS (1999) Auto-inactivation by cleavage within the dimer interface of Kaposi’s sarcoma-associated herpesvirus protease. J Mol Biol 289: 197–203. 10366498

24. Loveland AN, Chan C-K, Brignole EJ, Gibson W (2005) Cleavage of human cytomegalovirus protease pUL80a at internal and cryptic sites is not essential but enhances infectivity. J Virol 79: 12961–12968. 16188998

25. Holwerda BC, Wittwer AJ, Duffin KL, Smith C, Toth MV, et al. (1994) Activity of two-chain recombinant human cytomegalovirus protease. J Biol Chem 269: 25911–25915. 7929296

26. Waxman L, Darke PL (2000) The herpesvirus proteases as targets for antiviral chemotherapy. Antivir Chem Chemother 11: 1–22. 10693650

27. Darke PL, Cole JL, Waxman L, Hall DL, Sardana MK, et al. (1996) Active human cytomegalovirus protease is a dimer. J Biol Chem 271: 7445–7449. 8631772

28. Nomura AM, Marnett AB, Shimba N, Dotsch V, Craik CS (2005) Induced structure of a helical switch as a mechanism to regulate enzymatic activity. Nat Struct Mol Biol 12: 1019–1020. 16244665

29. Plafker SM, Gibson W (1998) Cytomegalovirus assembly protein precursor and proteinase precursor contain two nuclear localization signals that mediate their own nuclear translocation and that of the major capsid protein. J Virol 72: 7722–7732. 9733808

30. Robertson BJ, McCann PJ, Matusick-Kumar L, Newcomb WW, Brown JC, et al. (1996) Separate functional domains of the herpes simplex virus type 1 protease: evidence for cleavage inside capsids. J Virol 70: 4317–4328. 8676454

31. Tong L, Qian C, Massariol M-J, Bonneau PR, Cordingley MG, et.al (1996) A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature 383: 272–275. 8805706

32. Qiu X, Culp JS, DiLella AG, Hellmig B, Hoog SS, et al. (1996) Unique fold and active site in cytomegalovirus protease. Nature 383: 275–279. 8805707

33. Shieh H-S, Kurumbail RG, Stevens AM, Stegeman RA, Sturman EJ, et al. (1996) Three-dimensional structure of human cytomegalovirus protease. Nature 383: 279–282. 8805708

34. Hoog SS, Smith WW, Qiu X, Janson CA, Hellmig B, et al. (1997) Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex. Biochemistry 36: 14023–14029. 9369473

35. Qiu X, Janson CA, Culp JS, Richardson SB, Debouck C, et al. (1997) Crystal structure of varicella-zoster virus protease. Proc Natl Acad Sci U S A 94: 2874–2879. 9096314

36. Reiling KK, Pray TR, Craik CS, Stroud RM (2000) Functional consequences of the Kaposi's sarcoma-associated herpesvirus protease structure: regulation of activity and dimerization by conserved structural elements. Biochemistry 39: 12796–12803. 11041844

37. Buisson M, Hernandez J-F, Lascoux D, Schoehn G, Forest E, et al. (2002) The crystal structure of the Epstein-Barr virus protease shows rearrangement of the processed C terminus. J Mol Biol 324: 89–103. 12421561

38. Lazic A, Goetz DH, Nomura AM, Marnett AB, Craik CS (2007) Substrate modulation of enzyme activity in the herpesvirus protease family. J Mol Biol 373: 913–923. 17870089

39. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539. doi: 10.1038/msb.2011.75 21988835

40. Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, et al. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38: W695–W699. doi: 10.1093/nar/gkq313 20439314

41. Batra R, Khayat R, Tong L (2001) Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease. Nat Struct Mol Biol 8: 810–817.

42. Liang P, Brun KA, Feild JA, O'Donnell K, Doyle ML, et al. (1998) Site-Directed Mutagenesis Probing the Catalytic Role of Arginines 165 and 166 of Human Cytomegalovirus Protease. Biochemistry 37: 5923–5929. 9558326

43. Lee GM, Shahian T, Baharuddin A, Gable JE, Craik CS (2011) Enzyme inhibition by allosteric capture of an inactive conformation. J Mol Biol 411: 999–1016. doi: 10.1016/j.jmb.2011.06.032 21723875

44. Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, et al. (2014) Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry 53: 4648–4660. doi: 10.1021/bi5003234 24977643

45. Shahian T, Lee GM, Lazic A, Arnold LA, Velusamy P, et al. (2009) Inhibition of a viral enzyme by a small-molecule dimer disruptor. Nat Chem Biol 5: 640–646. doi: 10.1038/nchembio.192 19633659

46. Conway JF, Homa FL Nucleocapsid structure, assembly and DNA packaging of Herpes simplex virus. In: Weller SK, editors. Alphaherpesviruses: Molecular Virology. Norfolk, UK: Caister Academic Press; 2011. pp. 175–193.

47. Gibson W. Chapter 783—Cytomegalovirus assemblin and precursor. In: Rawlings ND, Salvesen GS, editors. Handbook of proteolytic enzymes. London: Academic Press, Elsevier; 2013. pp. 3540–3545.

48. Shahian T. Craik CS. Chapter 784—Kaposi's Sarcoma Virus Assemblin (Herpesvirus 8-type Assemblin). In: Rawlings ND, Salvesen GS, editors. Handbook of proteolytic enzymes. London: Academic Press, Elsevier; 2013. pp. 3545–3550.

49. Jupp R, Mills J, Tigue NJ, Kay J. Chapter 785—Human Herpesvirus Type 6 Assemblin. In: Rawlings ND, Salvesen GS, editors. Handbook of proteolytic enzymes. London: Academic Press, Elsevier; 2013. pp. 3550–3552.

50. Jupp R, Ritchie A, Robinson M, Broadhurst A, Mills J. Chapter 786—Epstein-Barr Virus Assemblin. In: Rawlings ND, Salvesen GS, editors. Handbook of proteolytic enzymes. London: Academic Press, Elsevier; 2013. pp. 3552–3554.

51. McMillan D, Jupp R, Mills J, Kay J. Chapter 787—Varicella-Zoster Virus Assemblin. In: Rawlings ND, Salvesen GS, editors. Handbook of proteolytic enzymes. London: Academic Press, Elsevier; 2013. pp. 3555–3556.

52. Steven AC, Spear PG. Herpesvirus capsid assembly and envelopment. In: Chiu W, Burnett RM, Garcea RL, editors. Structural Biology of Viruses. New York, NY: Oxford University Press; 1997. pp. 312–351.

53. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774–797. 17681537

54. Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256–2268. 15572779

55. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, et al. (2009) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66 (Pt 1): 12–21. doi: 10.1107/S0907444909042073 20057044

56. Khayat R, Batra R, Massariol M, Lagacé L, Tong L (2001) Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease. Biochemistry 40: 6344–6351. 11371196

57. Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci U S A 93: 13–20. 8552589

58. Goodsell DS, Olson AJ (2000) Structural symmetry and protein function. Review. Annu Rev Biophys Biomol Struct 29: 105–153. 10940245

59. Diisopropyl fluorophosphate in the product catalogue from Sigma-Aldrich: http://www.sigmaaldrich.com/catalog/product/sigma/d0879

60. DiIanni CL, Stevens JT, Bolgar M, O'Boyle DR, Weinheimer SP, et al. (1994) Identification of the serine residue at the active site of the herpes simplex virus type 1 protease. J Biol Chem 269: 12672–12676. 8175677

61. Baum EZ, Bebernitz GA, Hulmes JD, Muzithras VP, Jones TR, et al. (1993) Expression and analysis of the human cytomegalovirus UL80-encoded protease: identification of autoproteolytic sites. J Virol 67: 497–506. 8380089

62. Smith MC, Giordano J, Cook JA, Wakulchik M, Villarreal EC, et al. (1994) Purification and kinetic characterization of human cytomegalovirus assemblin. Meth Enzymol 244: 412–423. 7845223

63. Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Cryst 36: 1277–1282.

64. Svergun DI (1996) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76: 2879–2886.

65. Ma B, Nussinov R (2007) Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr Top Med Chem 10: 999–1005.

66. Register RB, Shafer JA (1996) A facile system for construction of HSV-1 variants: site directed mutation of the UL26 protease gene in HSV-1. J Virol Methods 57: 181–193. 8801230

67. Palm GJ, Zdanov A, Gaitanaris GA, Stauber R, Pavlakis GN, et al. (1997) The structural basis for spectral variations in green fluorescent protein. Nat Struct Mol Biol 4: 361–365.

68. Mueller U, Darowski N, Fuchs MR, Förster R, Hellmig M, Paithankar KS, et al. (2012) Facilities for Macromolecular Crystallography at the Helmholtz-Zentrum Berlin. J Synch Rad 19: 442–449.

69. Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66 (Pt 2): 125–132. doi: 10.1107/S0907444909047337 20124692

70. Evans PR (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr D Biol Crystallogr 67 (Pt 4): 282–292. doi: 10.1107/S090744491003982X 21460446

71. Evans PR, Murshudov GN (2013) How good are my data and what is the resolution?. Acta Crystallogr D Biol Crystallogr 69 (Pt 7): 1204–1214. doi: 10.1107/S0907444913000061 23793146

72. Evans P (2005) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62 (Pt 1): 72–82. 16369096

73. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67 (Pt 4): 235–242. doi: 10.1107/S0907444910045749 21460441

74. Potterton EA, Briggs PJ, Turkenburg MG, Dodson EJ (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr D Biol Crystallogr 59 (Pt 7): 1131–1137. 12832755

75. Kantardjieff KA, Rupp B (2003) Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci 12: 1865–1871. 12930986

76. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33: 491–497. 5700707

77. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674. 19461840

78. Stein N (2008) CHAINSAW: a program for mutating pdb files used as templates in molecular replacement. J Appl Crystallogr 41: 641–643.

79. Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L (2004) The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr 60 (Pt 7): 1229–1236. 15213384

80. Emsley P, Lohkamp B, Scott W, Cowtan KD (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66 (Pt 4): 486–501. doi: 10.1107/S0907444910007493 20383002

81. Winn MD, Murshudov GN, Papiz MZ (2003) Macromolecular TLS Refinement in REFMAC at Moderate Resolutions. Methods Enzymol 374: 300–321. 14696379

82. Skubák P, Murshudov GN, Pannu NS (2004) Direct incorporation of experimental phase information in model refinement. Acta Crystallogr D Biol Crystallogr 60 (Pt 12 Pt 1): 2196–2201. 15572772

83. Murshudov GN, Vagin AA, Lebedev A, Wilson KS, Dodson EJ (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr D Biol Crystallogr 55 (Pt 1): 247–255. 10089417

84. Steiner RA, Lebedev AA, Murshudov GN (2003) Fisher's information in maximum-likelihood macromolecular crystallographic refinement. Acta Crystallogr D Biol Crystallogr 59 (Pt 12): 2114–2124. 14646069

85. Pannu NS, Murshudov GN, Dodson EJ, Read RJ (1998) Incorporation of prior phase information strengthens maximum-likelihood structure refinement. Acta Crystallogr D Biol Crystallogr 54 (Pt 6 Pt 2): 1285–1294. 10089505

86. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53 (Pt 3): 240–255. 15299926

87. Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, et al. (2004) REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr 60 (Pt 12 Pt 1): 2184–2195. 15572771

88. Winn MD, Isupov MN, Murshudov GN (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D Biol Crystallogr 57 (Pt 1): 122–133. 11134934

89. Schrödinger, LLC (2014) The PyMOL Molecular Graphics System, Version 1.7.1.3.

90. Blanchet CE, Spilotros A, Schwemmer F, Graewert MA, Kikhney A (2015) Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY). J Appl Cryst 48: 431–443.

91. Petoukhov MV, Franke D, Shkumatov A, Tria G, Kikhney AG, et al. (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Cryst 45: 342–350.

92. Franke D, Svergun DI (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Cryst 42: 342–346.

93. Volkov VV, Svergun DI (2003) Uniqueness of ab initio shape determination in small-angle scattering. J Appl Cryst 36: 860–864.

94. Valentini E, Kikhney AG, Previtaly G, Jeffries CM, Svergun DI (2015) SASBDB, a repository for biological small-angle scattering data. Nucl Acids Res 43: D357–D363. doi: 10.1093/nar/gku1047 25352555

95. Rawlings ND, Waller M, Barrett AJ, Bateman A (2014) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucl Acids Res 42: D503–D509. doi: 10.1093/nar/gkt953 24157837

96. Bond CS, Schüttelkopf AW (2009) ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments. Acta Crystallogr D Biol Crystallogr 65: 510–512. doi: 10.1107/S0907444909007835 19390156

97. Kozin MB, Svergun DI (2001) Automated matching of high- and low-resolution structural models. J Appl Cryst 34: 33–41.

Štítky
Hygiena a epidemiológia Infekčné lekárstvo Laboratórium

Článok vyšiel v časopise

PLOS Pathogens


2015 Číslo 7
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#