Abstract
Mono-ADP-ribosylation is a post-translational protein modification catalyzed by bacterial toxins and exoenzymes that function as ADP-ribosyltransferases. Despite the importance of this modification, the reaction mechanism remains poorly understood due to a lack of information on the crystal structure of these enzymes in complex with a substrate protein. Recently, the structures of two such complexes became available, which shed new light on the mechanisms of mono-ADP-ribosylation. In this review, we consider the reaction mechanism based on the structures of ADP-ribosyltransferases in complex with a substrate protein.
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References
Aktories K, Barmann M, Ohishi I, Tsuyama S, Jakobs KH, Habermann E (1986) Botulinum C2 toxin ADP-ribosylates actin. Nature 322(6077):390–392
Aktories K, Braun U, Rosener S, Just I, Hall A (1989) The rho gene product expressed in E. coli is a substrate of botulinum ADP-ribosyltransferase C3. Biochem Biophys Res Commun 158(1):209–213
Aktories K, Frevert J (1987) ADP-ribosylation of a 21-24 kDa eukaryotic protein(s) by C3, a novel botulinum ADP-ribosyltransferase, is regulated by guanine nucleotide. Biochem J 247(2):363–368
Aktories K, Lang AE, Schwan C, Mannherz HG (2011) Actin as target for modification by bacterial protein toxins. FEBS J 278(23):4526–4543
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Nat. Acad Sci USA 98(18):10037–10041
Barth H, Preiss JC, Hofmann F, Aktories K (1998) Characterization of the catalytic site of the ADP-ribosyltransferase Clostridium botulinum C2 toxin by site-directed mutagenesis. J Biol Chem 273(45):29506–29511
Berti PJ, Blanke SR, Schramm VL (1997) Transition state structure for the hydrolysis of NAD catalyzed by diphtheria toxin. J Am Chem Soc 119(50):12079–12088
Bokoch GM, Katada T, Northup JK, Hewlett EL, Gilman AG (1983) Identification of the predominant substrate for ADP-ribosylation by islet activating protein. J Biol Chem 258(4):2072–2075
Bubb MR, Govindasamy L, Yarmola EG, Vorobiev SM, Almo SC, Somasundaram T, Chapman MS, Agbandje-McKenna M, McKenna R (2002) Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-Å resolution. J Biol Chem 277(23):20999–21006
Buckley N, Handlon AL, Malby D, Burlingame AL, Oppenheimer NJ (1994) J Org Chem 59:3609–3615
Cassel D, Pfeuffer T (1978) Mechanism of cholera toxin action: covalent modification of the guanyl nucleotide-binding protein of the adenylate cyclase system. Proc Nat Acad Sci USA 75(6):2669–2673
Chung DW, Collier RJ (1977) Enzymatically active peptide from the adenosine diphosphate-ribosylating toxin of Pseudomonas aeruginosa. Infect Immun 16(3):832–841
Domenighini M, Magagnoli C, Pizza M, Rappuoli R (1994) Common features of the NAD-binding and catalytic site of ADP-ribosylating toxins. Mol Microbiol 14(1):41–50
Domenighini M, Rappuoli R (1996) Three conserved consensus sequences identify the NAD-binding site of ADP-ribosylating enzymes, expressed by eukaryotes, bacteria and T-even bacteriophages. Mol Microbiol 21(4):667–674
Dominguez R (2004) Actin-binding proteins—a unifying hypothesis. Trends Biochem Sci 29(11):572–578
Etienne-Manneville S, Hall A (2002) Rho GTPases in cell biology. Nature 420(6916):629–635
Evans HR, Sutton JM, Holloway DE, Ayriss J, Shone CC, Acharya KR (2003) The crystal structure of C3stau2 from Staphylococcus aureus and its complex with NAD. J Biol Chem 278(46):45924–45930
Ferro AM, Oppenheimer NJ (1978) Structure of a poly (adenosine diphosphoribose) monomer: 2’-(5”-hosphoribosyl)-5’-adenosine monophosphate. Proc Nat Acad Sci USA 75(2):809–813
Fu ZQ, Guo M, Jeong BR, Tian F, Elthon TE, Cerny RL, Staiger D, Alfano JR (2007) A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity. Nature 447(7142):284–288
Fujii T, Iwane AH, Yanagida T, Namba K (2010) Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature 467(7316):724–728
Gallivan JP, Dougherty DA (1999) Cation-pi interactions in structural biology. Proc Nat Acad Sci USA 96(17):9459–9464
Gebeyehu G, Marquez VE, Kelley JA, Cooney DA, Jayaram HN, Johns DG (1983) Synthesis of thiazole-4-carboxamide adenine dinucleotide. A powerful inhibitor of IMP dehydrogenase. J Med Chem 26(6):922–925
Han S, Arvai AS, Clancy SB, Tainer JA (2001) Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis. J Mol Biol 305(1):95–107
Han S, Craig JA, Putnam CD, Carozzi NB, Tainer JA (1999) Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex. Nat Struct Biol 6(10):932–936
Hassa PO, Haenni SS, Elser M, Hottiger MO (2006) Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev: MMBR 70(3):789–829
Hochmann H, Pust S, von Figura G, Aktories K, Barth H (2006) Salmonella enterica SpvB ADP-ribosylates actin at position arginine-177-characterization of the catalytic domain within the SpvB protein and a comparison to binary clostridial actin-ADP-ribosylating toxins. Biochemistry 45(4):1271–1277
Holbourn KP, Sutton JM, Evans HR, Shone CC, Acharya KR (2005) Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase. Proc Nat Acad Sci USA 102(15):5357–5362
Holmes KC, Popp D, Gebhard W, Kabsch W (1990) Atomic model of the actin filament. Nature 347(6288):44–49
Honjo T, Nishizuka Y, Hayaishi O (1968) Diphtheria toxin-dependent adenosine diphosphate ribosylation of aminoacyl transferase II and inhibition of protein synthesis. J Biol Chem 243(12):3553–3555
Honjo T, Nishizuka Y, Kato I, Hayaishi O (1971) Adenosine diphosphate ribosylation of aminoacyl transferase II and inhibition of protein synthesis by diphtheria toxin. J Biol Chem 246(13):4251–4260
Hottiger MO, Hassa PO, Luscher B, Schuler H, Koch-Nolte F (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem Sci 35(4):208–219
Iglewski BH, Kabat D (1975) NAD-dependent inhibition of protein synthesis by Pseudomonas aeruginosa toxin. Proc Nat Acad Sci USA 72(6):2284–2288
Jank T, Aktories K (2013) Strain-alleviation model of ADP-ribosylation. Proc Nat Acad Sci USA 110(11):4163–4164
Jørgensen R, Merrill AR, Yates SP, Marquez VE, Schwan AL, Boesen T, Andersen GR (2005) Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature 436(7053):979–984
Jørgensen R, Wang Y, Visschedyk D, Merrill AR (2008) The nature and character of the transition state for the ADP-ribosyltransferase reaction. EMBO Rep 9(8):802–809
Kabsch W, Mannherz HG, Suck D, Pai EF, Holmes KC (1990) Atomic structure of the actin:DNase I complex. Nature 347(6288):37–44
Kahn RA, Gilman AG (1986) The protein cofactor necessary for ADP-ribosylation of Gs by cholera toxin is itself a GTP binding protein. J Biol Chem 261(17):7906–7911
Katada T, Ui M (1982) ADP ribosylation of the specific membrane protein of C6 cells by islet-activating protein associated with modification of adenylate cyclase activity. J Biol Chem 257(12):7210–7216
Kimoto H, Fujii Y, Hirano S, Yokota Y, Taketo A (2006) Genetic and biochemical properties of streptococcal NAD-glycohydrolase inhibitor. J Biol Chem 281(14):9181–9189
Koch-Nolte F, Kernstock S, Mueller-Dieckmann C, Weiss MS, Haag F (2008) Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolases. Front Biosci: J Virtual Libr 13:6716–6729
Lang AE, Schmidt G, Schlosser A, Hey TD, Larrinua IM, Sheets JJ, Mannherz HG, Aktories K (2010) Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering. Science 327(5969):1139–1142
Margarit SM, Davidson W, Frego L, Stebbins CE (2006) A steric antagonism of actin polymerization by a salmonella virulence protein. Structure 14(8):1219–1229
McLaughlin PJ, Gooch JT, Mannherz HG, Weeds AG (1993) Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature 364(6439):685–692
Menetrey J, Flatau G, Stura EA, Charbonnier JB, Gas F, Teulon JM, Le Du MH, Boquet P, Menez A (2002) NAD binding induces conformational changes in Rho ADP-ribosylating Clostridium botulinum C3 exoenzyme. J Biol Chem 277(34):30950–30957
Moss J, Garrison S, Oppenheimer NJ, Richardson SH (1979a) NAD-dependent ADP-ribosylation of arginine and proteins by Escherichia coli heat-labile enterotoxin. J Biol Chem 254(14):6270–6272
Moss J, Stanley SJ, Oppenheimer NJ (1979b) Substrate specificity and partial purification of a stereospecific NAD- and guanidine-dependent ADP-ribosyltransferase from avian erythrocytes. J Biol Chem 254(18):8891–8894
Moss J, Stanley SJ, Vaughan M, Tsuji T (1993) Interaction of ADP-ribosylation factor with Escherichia coli enterotoxin that contains an inactivating lysine 112 substitution. J Biol Chem 268(9):6383–6387
Murakami K, Yasunaga T, Noguchi TQ, Gomibuchi Y, Ngo KX, Uyeda TQ, Wakabayashi T (2010) Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell 143(2):275–287
Nagahama M, Sakaguchi Y, Kobayashi K, Ochi S, Sakurai J (2000) Characterization of the enzymatic component of Clostridium perfringens iota-toxin. J Bacteriol 182(8):2096–2103
Noda M, Tsai SC, Adamik R, Moss J, Vaughan M (1990) Mechanism of cholera toxin activation by a guanine nucleotide-dependent 19 kDa protein. Biochim Biophys Acta 1034(2):195–199
O’Neal CJ, Jobling MG, Holmes RK, Hol WG (2005) Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 309(5737):1093–1096
Oppenheimer NJ (1994) NAD hydrolysis: chemical and enzymatic mechanisms. Mol Cell Biochem 138(1–2):245–251
Oppenheimer NJ, Bodley JW (1981) Diphtheria toxin. Site and configuration of ADP-ribosylation of diphthamide in elongation factor 2. J Biol Chem 256(16):8579–8581
Otterbein LR, Cosio C, Graceffa P, Dominguez R (2002) Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system. Proc Nat Acad Sci USA 99(12):8003–8008
Perelle S, Domenighini M, Popoff MR (1996) Evidence that Arg-295, Glu-378, and Glu-380 are active-site residues of the ADP-ribosyltransferase activity of iota toxin. FEBS Lett 395(2–3):191–194
Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC (2010) Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol 170(3):427–438
Popoff MR, Milward FW, Bancillon B, Boquet P (1989) Purification of the Clostridium spiroforme binary toxin and activity of the toxin on HEp-2 cells. Infect Immun 57(8):2462–2469
Popoff MR, Rubin EJ, Gill DM, Boquet P (1988) Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain. Infect Immun 56(9):2299–2306
Schleberger C, Hochmann H, Barth H, Aktories K, Schulz GE (2006) Structure and action of the binary C2 toxin from Clostridium botulinum. J Mol Biol 364(4):705–715
Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U (1993) The structure of crystalline profilin-beta-actin. Nature 365(6449):810–816
Sekine A, Fujiwara M, Narumiya S (1989) Asparagine residue in the rho gene product is the modification site for botulinum ADP-ribosyltransferase. J Biol Chem 264(15):8602–8605
Shniffer A, Visschedyk DD, Ravulapalli R, Suarez G, Turgeon ZJ, Petrie AA, Chopra AK, Merrill AR (2012) Characterization of an actin-targeting ADP-ribosyltransferase from Aeromonas hydrophila. J Biol Chem 287(44):37030–37041
Sixma TK, Pronk SE, Kalk KH, Wartna ES, van Zanten BA, Witholt B, Hol WG (1991) Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli. Nature 351(6325):371–377
Sternweis PC, Robishaw JD (1984) Isolation of two proteins with high affinity for guanine nucleotides from membranes of bovine brain. J Biol Chem 259(22):13806–13813
Sun J, Maresso AW, Kim JJ, Barbieri JT (2004) How bacterial ADP-ribosylating toxins recognize substrates. Nat Struct Mol Biol 11(9):868–876
Sundriyal A, Roberts AK, Shone CC, Acharya KR (2009) Structural basis for substrate recognition in the enzymatic component of ADP-ribosyltransferase toxin CDTa from Clostridium difficile. J Biol Chem 284(42):28713–28719
Tsuge H, Nagahama M, Nishimura H, Hisatsune J, Sakaguchi Y, Itogawa Y, Katunuma N, Sakurai J (2003) Crystal structure and site-directed mutagenesis of enzymatic components from Clostridium perfringens iota-toxin. J Mol Biol 325(3):471–483
Tsuge H, Nagahama M, Oda M, Iwamoto S, Utsunomiya H, Marquez VE, Katunuma N, Nishizawa M, Sakurai J (2008) Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens iota-toxin. Proc Nat Acad Sci USA 105(21):7399–7404
Tsurumura T, Tsumori Y, Qiu H, Oda M, Sakurai J, Nagahama M, Tsuge H (2013) Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex. Proc Nat Acad Sci USA 110(11):4267–4272
Vandekerckhove J, Schering B, Barmann M, Aktories K (1987) Clostridium perfringens iota toxin ADP-ribosylates skeletal muscle actin in Arg-177. FEBS Lett 225(1–2):48–52
Visschedyk D, Rochon A, Tempel W, Dimov S, Park HW, Merrill AR (2012) Certhrax toxin, an anthrax-related ADP-ribosyltransferase from Bacillus cereus. J Biol Chem 287(49):41089–41102
Vogelsgesang M, Stieglitz B, Herrmann C, Pautsch A, Aktories K (2008) Crystal structure of the Clostridium limosum C3 exoenzyme. FEBS Lett 582(7):1032–1036
Wilde C, Just I, Aktories K (2002) Structure-function analysis of the Rho-ADP-ribosylating exoenzyme C3stau2 from Staphylococcus aureus. Biochemistry 41(5):1539–1544
Zhang RG, Scott DL, Westbrook ML, Nance S, Spangler BD, Shipley GG, Westbrook EM (1995) The three-dimensional crystal structure of cholera toxin. J Mol Biol 251(4):563–573
Acknowledgments
H.T. appreciates Masahiro Nagahama, Masataka Oda, and Jun Sakurai, who support our work on the structure of ART, and Nobuhiko Katunuma for his continuous research support. This work was supported in part by a Strategic Research Foundation Grant-aided Project for Private Universities and Grant-in-Aid for Scientific Research on Innovative Areas, MEXT/JSPS KAKENHI Grant Number: 25121733 of Japan.
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Tsuge, H., Tsurumura, T. (2014). Reaction Mechanism of Mono-ADP-Ribosyltransferase Based on Structures of the Complex of Enzyme and Substrate Protein. In: Koch-Nolte, F. (eds) Endogenous ADP-Ribosylation. Current Topics in Microbiology and Immunology, vol 384. Springer, Cham. https://doi.org/10.1007/82_2014_415
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