Summary: Diphtheria toxin, R domain
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Diphtheria toxin Edit Wikipedia article
|Diphtheria toxin, C domain|
complex of diphtheria toxin and heparin-binding epidermal growth factor
|Diphtheria toxin, T domain|
complex of diphtheria toxin and heparin-binding epidermal growth factor
|Diphtheria toxin, R domain|
complex of diphtheria toxin and heparin-binding epidermal growth factor
|tox diphtheria toxin precursor|
|Chromosome||genome: 0.19 - 0.19 Mb|
Diphtheria toxin is an exotoxin secreted by Corynebacterium diphtheriae, the pathogenic bacterium that causes diphtheria. Unusually, the toxin gene is encoded by a bacteriophage (a virus that infects bacteria). The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis.
Diphtheria toxin is a single polypeptide chain of 535 amino acids consisting of two subunits linked by disulfide bridges, known as an A-B toxin. Binding to the cell surface of the B subunit (the less stable of the two subunits) allows the A subunit (the more stable part of the protein) to penetrate the host cell.
The crystal structure of the diphtheria toxin homodimer has been determined to 2.5 Ångstrom resolution. The structure reveals a Y-shaped molecule consisting of three domains. Fragment A contains the catalytic C domain, and fragment B consists of the T and R domains:
- The amino-terminal catalytic domain, known as the C domain, has an unusual beta+alpha fold. The C domain blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of eukaryotic elongation factor 2 (eEF-2).
- A central translocation domain, known as the T domain or TM domain, has a multi-helical globin-like fold with two additional helices at the amino terminus but no counterpart to the first globin helix. This domain is thought to unfold in the membrane. A pH-induced conformational change in the T domain triggers insertion into the endosomal membrane and facilitates the transfer of the C domain into the cytoplasm.
- A carboxy-terminal receptor-binding domain, known as the R domain, has a beta-sandwich fold consisting of nine strands in two sheets with Greek-key topology; it is a subclass of immunoglobulin-like fold. The R domain binds to a cell surface receptor, permitting the toxin to enter the cell by receptor-mediated endocytosis.
- The leader region is cleaved during secretion.
- Proteolytic nicking separates A and B subunits, which remain joined by disulfide bonds until they reach the cytosol.
- The toxin binds to heparin-binding epidermal growth factor precursor (HB-EGF).
- The complex undergoes endocytosis by the host cell.
- Acidification inside the endosome induces translocation of the A subunit into the cytosol.
- Disulfide bonds are broken.
- The B subunit remains in the endosome as a pore.
- A subunit ADP-ribosylates host eEF-2. eEF-2 is required for protein synthesis; when it is inactivated, the host cannot make protein and thus dies.
The diphtheria toxin has the same mechanism of action as the enzyme NAD(+)—diphthamide ADP-ribosyltransferase (EC 22.214.171.124). It catalyzes the transfer of NAD+ to a diphthamide residue in eEF-2, inactivating this protein. It does so by ADP-ribosylating the unusual amino acid diphthamide. In this way, it acts as a RNA translational inhibitor. The catalysed reaction is as follows:
- NAD+ + peptide diphthamide nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide.
Lethal dose and effects
Diphtheria toxin is extraordinarily potent. The lethal dose for humans is about 0.1 μg of toxin per kg of body weight. Death occurs through necrosis of the heart and liver. Diphtheria toxin has also been associated with the development of myocarditis. Myocarditis secondary to diphtheria toxin is considered one of the biggest risks to unimmunized children.
Diphtheria toxin was discovered in 1888 by Émile Roux and Alexandre Yersin. In 1890 Emil Adolf von Behring developed an anti-toxin based on blood. In 1951, Freeman found that the toxin gene was not encoded on the bacterial chromosome, but by a lysogenic phage infecting all toxigenic strains.
Similar to other A-B toxins, diphtheria toxin is adept at transporting exogenous proteins across mammalian cell membranes, which are usually impermeable to large proteins. This unique ability can be repurposed to deliver therapeutic proteins, instead of the catalytic domain of the toxin.
- TABLE 1. Bacterial virulence properties altered by bacteriophages from Patrick L. Wagner; Matthew K. Waldor (August 2002). "Bacteriophage Control of Bacterial Virulence". Infection and Immunity. 70 (8): 3985–3993. PMC . PMID 12117903. doi:10.1128/IAI.70.8.3985-3993.2002.
- Bell CE, Eisenberg D (1996). "Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide". Biochemistry. 35 (4): 1137–1149. PMID 8573568. doi:10.1021/bi9520848.
- Murphy JR (1996). "Corynebacterium Diphtheriae: Diphtheria Toxin Production". In Baron S; et al. Medical microbiology (4th ed.). Galveston, Texas: Univ. of Texas Medical Branch. ISBN 0-9631172-1-1.
- Choe S, Bennett MJ, Fujii G, Curmi PM, Kantardjieff KA, Collier RJ, Eisenberg D (May 1992). "The crystal structure of diphtheria toxin". Nature. 357 (6375): 216–22. PMID 1589020. doi:10.1038/357216a0.
- Bell CE, Eisenberg D (January 1997). "Crystal structure of nucleotide-free diphtheria toxin". Biochemistry. 36 (3): 481–8. PMID 9012663. doi:10.1021/bi962214s.
- Bennett MJ, Eisenberg D (September 1994). "Refined structure of monomeric diphtheria toxin at 2.3 A resolution". Protein Sci. 3 (9): 1464–75. PMC . PMID 7833808. doi:10.1002/pro.5560030912.
- Bell CE, Eisenberg D (January 1996). "Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide". Biochemistry. 35 (4): 1137–49. PMID 8573568. doi:10.1021/bi9520848.
- Bennett MJ, Choe S, Eisenberg D (September 1994). "Refined structure of dimeric diphtheria toxin at 2.0 A resolution". Protein Sci. 3 (9): 1444–63. PMC . PMID 7833807. doi:10.1002/pro.5560030911.
- Pappenheimer A (1977). "Diphtheria toxin.". Annu Rev Biochem. 46 (1): 69–94. PMID 20040. doi:10.1146/annurev.bi.46.070177.000441.
- Enke, U (2015): 125 Jahre Diphtherieheilserum, Dtsch Arztebl 2015; 112(49): A-2088
- Freeman VJ (June 1951). "Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae". J. Bacteriol. 61 (6): 675–88. PMC . PMID 14850426.
- Freeman VJ, Morse IU (March 1952). "Further observations on the change to virulence of bacteriophage-infected avirulent strains of Corynebacterium diphtheria". J. Bacteriol. 63 (3): 407–14. PMC . PMID 14927573.
- Diphtheria from Todar's Online Textbook of Bacteriology, Kenneth Todar 2009. Accessed 08 September 2010.
- Auger, Anick; Park, Minyoung; Nitschke, Felix; Minassian, Lori M.; Beilhartz, Greg L.; Minassian, Berge A.; Melnyk, Roman A. (2015-08-03). "Efficient Delivery of Structurally Diverse Protein Cargo into Mammalian Cells by a Bacterial Toxin". Molecular Pharmaceutics. 12 (8): 2962–2971. ISSN 1543-8392. PMID 26103531. doi:10.1021/acs.molpharmaceut.5b00233.
- Beilhartz, Greg L.; Sugiman-Marangos, Seiji N.; Melnyk, Roman A. (2017-10-15). "Repurposing bacterial toxins for intracellular delivery of therapeutic proteins". Biochemical Pharmacology. 142: 13–20. ISSN 1873-2968. PMID 28408344. doi:10.1016/j.bcp.2017.04.009.
- Diphtheria Toxin at the US National Library of Medicine Medical Subject Headings (MeSH)
- How Diphtheria Toxin Works - Animation
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C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR022404
This entry represents the C-terminal receptor-binding domain, also known as the R domain. This domain has a beta-sandwich fold consisiting of nine strands in two sheet with greek-key topology; it is a subclass of immunoglobin-like fold [PUBMED:9012663]. The R domain binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis [PUBMED:7833808, PUBMED:8573568].
Diphtheria toxin (EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis [PUBMED:8573568]. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows:
The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution [PUBMED:1589020]. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology [PUBMED:1589020]. The TM- and receptor binding-domains together constitute fragment B.
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|Seed source:||Sarah Teichmann|
|Author:||Finn RD, Bateman A, Griffiths-Jones SR|
|Number in seed:||1|
|Number in full:||2|
|Average length of the domain:||153.00 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||37.05 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Diphtheria_R domain has been found. There are 18 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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