4nc2

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Crystal structure of TcdB-B1 bound to B39 VHH

Structural highlights

4nc2 is a 2 chain structure with sequence from Clostridioides difficile and Lama glama. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TCDB_CLODI Precursor of a cytotoxin that targets and disrupts the colonic epithelium, inducing the host inflammatory and innate immune responses and resulting in diarrhea and pseudomembranous colitis (PubMed:20844489, PubMed:24919149). TcdB constitutes the main toxin that mediates the pathology of C.difficile infection, an opportunistic pathogen that colonizes the colon when the normal gut microbiome is disrupted (PubMed:19252482, PubMed:20844489). Compared to TcdA, TcdB is more virulent and more important for inducing the host inflammatory and innate immune responses (PubMed:19252482, PubMed:24919149). This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdB) into the host cytosol (PubMed:10768933, PubMed:11152463, PubMed:12941936, PubMed:17334356, PubMed:20498856). Targets colonic epithelia by binding to the frizzled receptors FZD1, FZD2 and FZD7, and enters host cells via clathrin-mediated endocytosis (PubMed:27680706). Frizzled receptors constitute the major host receptors in the colonic epithelium, but other receptors, such as CSPG4 or NECTIN3/PVRL3, have been identified (PubMed:25547119, PubMed:26038560, PubMed:27680706). Binding to carbohydrates and sulfated glycosaminoglycans on host cell surface also contribute to entry into cells (By similarity). Once entered into host cells, acidification in the endosome promotes the membrane insertion of the translocation region and formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane (PubMed:11152463, PubMed:12941936, PubMed:24567384). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdB), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356, PubMed:27571750).[UniProtKB:P16154][1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149, PubMed:7777059, PubMed:8144660). Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-alpha-D-glucose as the sugar donor (PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149, PubMed:7777059). Monoglucosylation of host small GTPases completely prevents the recognition of the downstream effector, blocking the GTPases in their inactive form, leading to actin cytoskeleton disruption and cell death, resulting in the loss of colonic epithelial barrier function (PubMed:24919149, PubMed:7777059).[14] [15] [16] [17] [18] [19]

Publication Abstract from PubMed

Clostridium difficile infection (CDI) is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function, and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

Structural Basis for Antibody Recognition in the Receptor-Binding Domains of Toxins A and B from Clostridium difficile.,Murase T, Eugenio L, Schorr M, Hussack G, Tanha J, Kitova EN, Klassen JS, Ng KK J Biol Chem. 2013 Dec 5. PMID:24311789[20]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
10 reviews cite this structure
Clostridium difficile infection.
Smits et al. (2016)
9 more
18 other articles
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See Also

References

  1. ↑ Qa'Dan M, Spyres LM, Ballard JD. pH-induced conformational changes in Clostridium difficile toxin B. Infect Immun. 2000 May;68(5):2470-4. doi: 10.1128/IAI.68.5.2470-2474.2000. PMID:10768933 doi:http://dx.doi.org/10.1128/IAI.68.5.2470-2474.2000
  2. ↑ Barth H, Pfeifer G, Hofmann F, Maier E, Benz R, Aktories K. Low pH-induced formation of ion channels by clostridium difficile toxin B in target cells. J Biol Chem. 2001 Apr 6;276(14):10670-6. doi: 10.1074/jbc.M009445200. Epub 2001 , Jan 4. PMID:11152463 doi:http://dx.doi.org/10.1074/jbc.M009445200
  3. ↑ Pfeifer G, Schirmer J, Leemhuis J, Busch C, Meyer DK, Aktories K, Barth H. Cellular uptake of Clostridium difficile toxin B. Translocation of the N-terminal catalytic domain into the cytosol of eukaryotic cells. J Biol Chem. 2003 Nov 7;278(45):44535-41. doi: 10.1074/jbc.M307540200. Epub 2003 , Aug 26. PMID:12941936 doi:http://dx.doi.org/10.1074/jbc.M307540200
  4. ↑ Reineke J, Tenzer S, Rupnik M, Koschinski A, Hasselmayer O, Schrattenholz A, Schild H, von Eichel-Streiber C. Autocatalytic cleavage of Clostridium difficile toxin B. Nature. 2007 Mar 22;446(7134):415-9. doi: 10.1038/nature05622. Epub 2007 Mar 4. PMID:17334356 doi:http://dx.doi.org/10.1038/nature05622
  5. ↑ Lyras D, O'Connor JR, Howarth PM, Sambol SP, Carter GP, Phumoonna T, Poon R, Adams V, Vedantam G, Johnson S, Gerding DN, Rood JI. Toxin B is essential for virulence of Clostridium difficile. Nature. 2009 Apr 30;458(7242):1176-9. doi: 10.1038/nature07822. Epub 2009 Mar 1. PMID:19252482 doi:http://dx.doi.org/10.1038/nature07822
  6. ↑ Papatheodorou P, Zamboglou C, Genisyuerek S, Guttenberg G, Aktories K. Clostridial glucosylating toxins enter cells via clathrin-mediated endocytosis. PLoS One. 2010 May 17;5(5):e10673. doi: 10.1371/journal.pone.0010673. PMID:20498856 doi:http://dx.doi.org/10.1371/journal.pone.0010673
  7. ↑ Kuehne SA, Cartman ST, Heap JT, Kelly ML, Cockayne A, Minton NP. The role of toxin A and toxin B in Clostridium difficile infection. Nature. 2010 Oct 7;467(7316):711-3. doi: 10.1038/nature09397. Epub 2010 Sep 15. PMID:20844489 doi:http://dx.doi.org/10.1038/nature09397
  8. ↑ Zhang Z, Park M, Tam J, Auger A, Beilhartz GL, Lacy DB, Melnyk RA. Translocation domain mutations affecting cellular toxicity identify the Clostridium difficile toxin B pore. Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3721-6. doi: , 10.1073/pnas.1400680111. Epub 2014 Feb 24. PMID:24567384 doi:http://dx.doi.org/10.1073/pnas.1400680111
  9. ↑ Xu H, Yang J, Gao W, Li L, Li P, Zhang L, Gong YN, Peng X, Xi JJ, Chen S, Wang F, Shao F. Innate immune sensing of bacterial modifications of Rho GTPases by the Pyrin inflammasome. Nature. 2014 Sep 11;513(7517):237-41. doi: 10.1038/nature13449. Epub 2014 Jun 11. PMID:24919149 doi:http://dx.doi.org/10.1038/nature13449
  10. ↑ Yuan P, Zhang H, Cai C, Zhu S, Zhou Y, Yang X, He R, Li C, Guo S, Li S, Huang T, Perez-Cordon G, Feng H, Wei W. Chondroitin sulfate proteoglycan 4 functions as the cellular receptor for Clostridium difficile toxin B. Cell Res. 2015 Feb;25(2):157-68. doi: 10.1038/cr.2014.169. Epub 2014 Dec 30. PMID:25547119 doi:http://dx.doi.org/10.1038/cr.2014.169
  11. ↑ LaFrance ME, Farrow MA, Chandrasekaran R, Sheng J, Rubin DH, Lacy DB. Identification of an epithelial cell receptor responsible for Clostridium difficile TcdB-induced cytotoxicity. Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7073-8. doi: , 10.1073/pnas.1500791112. Epub 2015 May 18. PMID:26038560 doi:http://dx.doi.org/10.1073/pnas.1500791112
  12. ↑ Chumbler NM, Rutherford SA, Zhang Z, Farrow MA, Lisher JP, Farquhar E, Giedroc DP, Spiller BW, Melnyk RA, Lacy DB. Crystal structure of Clostridium difficile toxin A. Nat Microbiol. 2016 Jan 11;1:15002. doi: 10.1038/nmicrobiol.2015.2. PMID:27571750 doi:http://dx.doi.org/10.1038/nmicrobiol.2015.2
  13. ↑ Tao L, Zhang J, Meraner P, Tovaglieri A, Wu X, Gerhard R, Zhang X, Stallcup WB, Miao J, He X, Hurdle JG, Breault DT, Brass AL, Dong M. Frizzled proteins are colonic epithelial receptors for C. difficile toxin B. Nature. 2016 Oct 20;538(7625):350-355. doi: 10.1038/nature19799. Epub 2016 Sep, 28. PMID:27680706 doi:http://dx.doi.org/10.1038/nature19799
  14. ↑ Jank T, Reinert DJ, Giesemann T, Schulz GE, Aktories K. Change of the donor substrate specificity of Clostridium difficile toxin B by site-directed mutagenesis. J Biol Chem. 2005 Nov 11;280(45):37833-8. doi: 10.1074/jbc.M506836200. Epub 2005 , Sep 12. PMID:16157585 doi:http://dx.doi.org/10.1074/jbc.M506836200
  15. ↑ Jank T, Giesemann T, Aktories K. Clostridium difficile glucosyltransferase toxin B-essential amino acids for substrate binding. J Biol Chem. 2007 Nov 30;282(48):35222-31. doi: 10.1074/jbc.M703138200. Epub 2007 , Sep 27. PMID:17901056 doi:http://dx.doi.org/10.1074/jbc.M703138200
  16. ↑ Genth H, Pauillac S, Schelle I, Bouvet P, Bouchier C, Varela-Chavez C, Just I, Popoff MR. Haemorrhagic toxin and lethal toxin from Clostridium sordellii strain vpi9048: molecular characterization and comparative analysis of substrate specificity of the large clostridial glucosylating toxins. Cell Microbiol. 2014 Nov;16(11):1706-21. doi: 10.1111/cmi.12321. Epub 2014 Aug 4. PMID:24905543 doi:http://dx.doi.org/10.1111/cmi.12321
  17. ↑ Xu H, Yang J, Gao W, Li L, Li P, Zhang L, Gong YN, Peng X, Xi JJ, Chen S, Wang F, Shao F. Innate immune sensing of bacterial modifications of Rho GTPases by the Pyrin inflammasome. Nature. 2014 Sep 11;513(7517):237-41. doi: 10.1038/nature13449. Epub 2014 Jun 11. PMID:24919149 doi:http://dx.doi.org/10.1038/nature13449
  18. ↑ Just I, Selzer J, Wilm M, von Eichel-Streiber C, Mann M, Aktories K. Glucosylation of Rho proteins by Clostridium difficile toxin B. Nature. 1995 Jun 8;375(6531):500-3. doi: 10.1038/375500a0. PMID:7777059 doi:http://dx.doi.org/10.1038/375500a0
  19. ↑ Just I, Fritz G, Aktories K, Giry M, Popoff MR, Boquet P, Hegenbarth S, von Eichel-Streiber C. Clostridium difficile toxin B acts on the GTP-binding protein Rho. J Biol Chem. 1994 Apr 8;269(14):10706-12. PMID:8144660
  20. ↑ Murase T, Eugenio L, Schorr M, Hussack G, Tanha J, Kitova EN, Klassen JS, Ng KK. Structural Basis for Antibody Recognition in the Receptor-Binding Domains of Toxins A and B from Clostridium difficile. J Biol Chem. 2013 Dec 5. PMID:24311789 doi:http://dx.doi.org/10.1074/jbc.M113.505917

Contents


PDB ID 4nc2

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