4nbz

From Proteopedia

(Difference between revisions)

Revision as of 08:20, 11 January 2023

Crystal Structure of TcdA-A1 Bound to A26.8 VHH

Structural highlights

4nbz is a 4 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.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TCDA_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). TcdA and TcdB constitute the main toxins that mediate 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 TcdB, TcdA is less virulent and less important for inducing the host inflammatory and innate immune responses (PubMed:19252482). This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdA) into the host cytosol (By similarity). Targets colonic epithelia by binding to some receptor, and enters host cells via clathrin-mediated endocytosis (By similarity). Binding to LDLR, as well as carbohydrates and sulfated glycosaminoglycans on host cell surface contribute to entry into cells (PubMed:1670930, PubMed:31160825, PubMed:16622409). In contrast to TcdB, Frizzled receptors FZD1, FZD2 and FZD7 do not act as host receptors in the colonic epithelium for TcdA (PubMed:27680706). 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 (By similarity). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdA), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356, PubMed:19553670, PubMed:27571750).[UniProtKB:P18177]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:7775453, PubMed:24905543, PubMed:30622517, PubMed:22747490, PubMed:22267739). Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, Rap2A 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:7775453, PubMed:24905543, PubMed:30622517, PubMed:22747490, PubMed:22267739). 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:7775453). Also able to catalyze monoglucosylation of some members of the Ras family (H-Ras/HRAS, K-Ras/KRAS and N-Ras/NRAS), but with much less efficiency than with Rho proteins, suggesting that it does not act on Ras proteins in vivo (PubMed:30622517).^[10] ^[11] ^[12] ^[13] ^[14]

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^[15]

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

References

↑ Greco A, Ho JG, Lin SJ, Palcic MM, Rupnik M, Ng KK. Carbohydrate recognition by Clostridium difficile toxin A. Nat Struct Mol Biol. 2006 May;13(5):460-1. Epub 2006 Apr 16. PMID:16622409 doi:http://dx.doi.org/10.1038/nsmb1084
↑ Tucker KD, Wilkins TD. Toxin A of Clostridium difficile binds to the human carbohydrate antigens I, X, and Y. Infect Immun. 1991 Jan;59(1):73-8. doi: 10.1128/iai.59.1.73-78.1991. PMID:1670930 doi:http://dx.doi.org/10.1128/iai.59.1.73-78.1991
↑ 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
↑ 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
↑ Pruitt RN, Chagot B, Cover M, Chazin WJ, Spiller B, Lacy DB. Structure-function analysis of inositol hexakisphosphate-induced autoprocessing in Clostridium difficile toxin A. J Biol Chem. 2009 Aug 14;284(33):21934-40. Epub 2009 Jun 24. PMID:19553670 doi:10.1074/jbc.M109.018929
↑ 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
↑ 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
↑ 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
↑ Tao L, Tian S, Zhang J, Liu Z, Robinson-McCarthy L, Miyashita SI, Breault DT, Gerhard R, Oottamasathien S, Whelan SPJ, Dong M. Sulfated glycosaminoglycans and low-density lipoprotein receptor contribute to Clostridium difficile toxin A entry into cells. Nat Microbiol. 2019 Oct;4(10):1760-1769. doi: 10.1038/s41564-019-0464-z. Epub, 2019 Jun 3. PMID:31160825 doi:http://dx.doi.org/10.1038/s41564-019-0464-z
↑ Pruitt RN, Chumbler NM, Rutherford SA, Farrow MA, Friedman DB, Spiller B, Lacy DB. Structural determinants of the Clostridium difficile toxin A glucosyltransferase activity. J Biol Chem. 2012 Jan 20. PMID:22267739 doi:10.1074/jbc.M111.298414
↑ D'Urzo N, Malito E, Biancucci M, Bottomley MJ, Maione D, Scarselli M, Martinelli M. The structure of Clostridium difficile TcdA-GT domain bound to Mn(2+) and UDP provides insight into glucosyltransferase activity and product release. FEBS J. 2012 Jul 2. doi: 10.1111/j.1742-4658.2012.08688.x. PMID:22747490 doi:10.1111/j.1742-4658.2012.08688.x
↑ 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
↑ Genth H, Junemann J, Lammerhirt CM, Lucke AC, Schelle I, Just I, Gerhard R, Pich A. Difference in Mono-O-Glucosylation of Ras Subtype GTPases Between Toxin A and Toxin B From Clostridioides difficile Strain 10463 and Lethal Toxin From Clostridium sordellii Strain 6018. Front Microbiol. 2018 Dec 21;9:3078. doi: 10.3389/fmicb.2018.03078. eCollection, 2018. PMID:30622517 doi:http://dx.doi.org/10.3389/fmicb.2018.03078
↑ Just I, Wilm M, Selzer J, Rex G, von Eichel-Streiber C, Mann M, Aktories K. The enterotoxin from Clostridium difficile (ToxA) monoglucosylates the Rho proteins. J Biol Chem. 1995 Jun 9;270(23):13932-6. doi: 10.1074/jbc.270.23.13932. PMID:7775453 doi:http://dx.doi.org/10.1074/jbc.270.23.13932
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4nbz"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of TcdA-A1 Bound to A26.8 VHH==
-<StructureSection load='4nbz' size='340' side='right' caption='[[4nbz]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='4nbz' size='340' side='right'caption='[[4nbz]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nbz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NBZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nbz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBZ FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nbx|4nbx]], [[4nby|4nby]], [[4nc0|4nc0]], [[4nc1|4nc1]], [[4nc2|4nc2]], [[2f6e|2f6e]]</td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbz OCA], [https://pdbe.org/4nbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbz RCSB], [https://www.ebi.ac.uk/pdbsum/4nbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbz ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tcdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935]), VHH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9844 Camelus glama])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbz OCA], [http://pdbe.org/4nbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nbz RCSB], [http://www.ebi.ac.uk/pdbsum/4nbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbz ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TCDA_CLODI TCDA_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). TcdA and TcdB constitute the main toxins that mediate 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 TcdB, TcdA is less virulent and less important for inducing the host inflammatory and innate immune responses (PubMed:19252482). This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdA) into the host cytosol (By similarity). Targets colonic epithelia by binding to some receptor, and enters host cells via clathrin-mediated endocytosis (By similarity). Binding to LDLR, as well as carbohydrates and sulfated glycosaminoglycans on host cell surface contribute to entry into cells (PubMed:1670930, PubMed:31160825, PubMed:16622409). In contrast to TcdB, Frizzled receptors FZD1, FZD2 and FZD7 do not act as host receptors in the colonic epithelium for TcdA (PubMed:27680706). 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 (By similarity). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdA), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356, PubMed:19553670, PubMed:27571750).[UniProtKB:P18177]<ref>PMID:16622409</ref> <ref>PMID:1670930</ref> <ref>PMID:17334356</ref> <ref>PMID:19252482</ref> <ref>PMID:19553670</ref> <ref>PMID:20844489</ref> <ref>PMID:27571750</ref> <ref>PMID:27680706</ref> <ref>PMID:31160825</ref>   Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:7775453, PubMed:24905543, PubMed:30622517, PubMed:22747490, PubMed:22267739). Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, Rap2A 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:7775453, PubMed:24905543, PubMed:30622517, PubMed:22747490, PubMed:22267739). 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:7775453). Also able to catalyze monoglucosylation of some members of the Ras family (H-Ras/HRAS, K-Ras/KRAS and N-Ras/NRAS), but with much less efficiency than with Rho proteins, suggesting that it does not act on Ras proteins in vivo (PubMed:30622517).<ref>PMID:22267739</ref> <ref>PMID:22747490</ref> <ref>PMID:24905543</ref> <ref>PMID:30622517</ref> <ref>PMID:7775453</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 17: @@
 </div>
 <div class="pdbe-citations 4nbz" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus difficilis hall and o'toole 1935]]
+[[Category: Clostridioides difficile]]
-[[Category: Camelus glama]]
+[[Category: Lama glama]]
-[[Category: Eugenio, L]]
+[[Category: Large Structures]]
-[[Category: Hussack, G]]
+[[Category: Eugenio L]]
-[[Category: Kitova, E N]]
+[[Category: Hussack G]]
-[[Category: Klassen, J S]]
+[[Category: Kitova EN]]
-[[Category: Murase, T]]
+[[Category: Klassen JS]]
-[[Category: Ng, K K.S]]
+[[Category: Murase T]]
-[[Category: Schorr, M]]
+[[Category: Ng KKS]]
-[[Category: Tanha, J]]
+[[Category: Schorr M]]
-[[Category: Antibody-antigen complex]]
+[[Category: Tanha J]]
-[[Category: Immune system]]

4nbz

From Proteopedia

Revision as of 08:20, 11 January 2023

Crystal Structure of TcdA-A1 Bound to A26.8 VHH

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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