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PDBsum entry 1tox

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protein ligands links
Toxin PDB id
1tox
Jmol
Contents
Protein chains
515 a.a.
Ligands
NAD ×2
Waters ×302
PDB id:
1tox
Name: Toxin
Title: Diphtheria toxin dimer complexed with NAD
Structure: Diphtheria toxin (dimeric). Chain: a, b. Synonym: dt. Other_details: ph=7.5, -180 deg c data collection
Source: Corynephage beta. Organism_taxid: 10703. Other_details: NAD from yeast, crystalline form, purchased sigma (n 1636)
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.227     R-free:   0.307
Authors: C.E.Bell,D.Eisenberg
Key ref:
C.E.Bell and D.Eisenberg (1996). Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Biochemistry, 35, 1137-1149. PubMed id: 8573568 DOI: 10.1021/bi9520848
Date:
06-Oct-95     Release date:   10-Jun-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00588  (DTX_CORBE) -  Diphtheria toxin
Seq:
Struc:
 
Seq:
Struc:
567 a.a.
515 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.36  - NAD(+)--diphthamide ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
+ diphthamide-[translation elongation factor 2]
= nicotinamide
+ N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9520848 Biochemistry 35:1137-1149 (1996)
PubMed id: 8573568  
 
 
Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.
C.E.Bell, D.Eisenberg.
 
  ABSTRACT  
 
Diphtheria toxin (DT), a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae, causes the disease diphtheria in humans by gaining entry into the cytoplasm of cells and inhibiting protein synthesis. Specifically, the catalytic (C) domain of DT transfers the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. In order to investigate how the C-domain of DT binds NAD and catalyzes the ADP-ribosylation of EF-2, the crystal structure of DT in complex with NAD has been determined to 2.3 A resolution. This is the first crystal structure of an ADP-ribosyltransferase (ADP-RT) enzyme in complex with NAD and suggests the features of the ADP-RT fold which are important for NAD binding. The conformation of NAD in the complex and the proximity of the Glu148 carboxylate group of the C-domain to the scissile, N-glycosidic bond of NAD suggest plausible modes of catalysis of the ADP-ribosylation reaction. Residues 39-46 of the active-site loop of the C-domain become disordered upon NAD binding, suggesting a potential role for this loop in the recognition of the ADP-ribose acceptor substrate, EF-2. The negatively charged phosphates and two ribose hydroxyls of NAD are not in direct contact with any atoms of the C-domain. Instead, they form an exposed surface which appears to be presented for recognition by EF-2. Structural alignments of the DT-NAD complex with the structures of other members of the ADP-RT family suggest how NAD may bind to these other enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22713970 B.A.Gibson, and W.L.Kraus (2012).
New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.
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20106667 M.O.Hottiger, P.O.Hassa, B.Lüscher, H.Schüler, and F.Koch-Nolte (2010).
Toward a unified nomenclature for mammalian ADP-ribosyltransferases.
  Trends Biochem Sci, 35, 208-219.  
19344187 R.J.Kreitman (2009).
Recombinant immunotoxins containing truncated bacterial toxins for the treatment of hematologic malignancies.
  BioDrugs, 23, 1.  
18851833 H.Kleine, E.Poreba, K.Lesniewicz, P.O.Hassa, M.O.Hottiger, D.W.Litchfield, B.H.Shilton, and B.Lüscher (2008).
Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-ribosylation.
  Mol Cell, 32, 57-69.  
18729382 J.B.French, Y.Cen, and A.A.Sauve (2008).
Plasmodium falciparum Sir2 is an NAD+-dependent deacetylase and an acetyllysine-dependent and acetyllysine-independent NAD+ glycohydrolase.
  Biochemistry, 47, 10227-10239.  
18349144 J.Baysarowich, K.Koteva, D.W.Hughes, L.Ejim, E.Griffiths, K.Zhang, M.Junop, and G.D.Wright (2008).
Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr.
  Proc Natl Acad Sci U S A, 105, 4886-4891.
PDB code: 2hw2
18583986 R.Jørgensen, Y.Wang, D.Visschedyk, and A.R.Merrill (2008).
The nature and character of the transition state for the ADP-ribosyltransferase reaction.
  EMBO Rep, 9, 802-809.
PDB codes: 2zit 3b78 3b82 3b8h
18019526 H.Lin (2007).
Nicotinamide adenine dinucleotide: beyond a redox coenzyme.
  Org Biomol Chem, 5, 2541-2554.  
17521358 K.K.Raju, H.S.Misra, and A.Sharma (2007).
Xanthomonas caspase displays an inherent PARP-like activity.
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16931513 A.R.Morrison, J.Moss, L.A.Stevens, J.E.Evans, C.Farrell, E.Merithew, D.G.Lambright, D.L.Greiner, J.P.Mordes, A.A.Rossini, and R.Bortell (2006).
ART2, a T cell surface mono-ADP-ribosyltransferase, generates extracellular poly(ADP-ribose).
  J Biol Chem, 281, 33363-33372.  
16892389 D.Bellocchi, G.Costantino, R.Pellicciari, N.Re, A.Marrone, and C.Coletti (2006).
Poly(ADP-ribose)-polymerase-catalyzed hydrolysis of NAD+: QM/MM simulation of the enzyme reaction.
  ChemMedChem, 1, 533-539.  
16956368 K.P.Holbourn, C.C.Shone, and K.R.Acharya (2006).
A family of killer toxins. Exploring the mechanism of ADP-ribosylating toxins.
  FEBS J, 273, 4579-4593.  
17025272 R.J.Kreitman (2006).
Immunotoxins for targeted cancer therapy.
  AAPS J, 8, E532-E551.  
  16511307 S.Kernstock, F.Koch-Nolte, J.Mueller-Dieckmann, M.S.Weiss, and C.Mueller-Dieckmann (2006).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of human ARH3, the first eukaryotic protein-ADP-ribosylhydrolase.
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16406634 S.P.Yates, R.Jørgensen, G.R.Andersen, and A.R.Merrill (2006).
Stealth and mimicry by deadly bacterial toxins.
  Trends Biochem Sci, 31, 123-133.  
16099990 C.J.O'Neal, M.G.Jobling, R.K.Holmes, and W.G.Hol (2005).
Structural basis for the activation of cholera toxin by human ARF6-GTP.
  Science, 309, 1093-1096.
PDB codes: 2a5d 2a5f 2a5g
16202152 H.Otto, P.A.Reche, F.Bazan, K.Dittmar, F.Haag, and F.Koch-Nolte (2005).
In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs).
  BMC Genomics, 6, 139.  
15611300 M.A.Steiger, J.E.Jackman, and E.M.Phizicky (2005).
Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism.
  RNA, 11, 99.  
16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.
  Nature, 436, 979-984.
PDB codes: 1zm2 1zm3 1zm4 1zm9
15611301 R.Sawaya, B.Schwer, and S.Shuman (2005).
Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1.
  RNA, 11, 107-113.  
14739238 A.W.Oliver, J.C.Amé, S.M.Roe, V.Good, G.de Murcia, and L.H.Pearl (2004).
Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2.
  Nucleic Acids Res, 32, 456-464.
PDB code: 1gs0
15489438 B.Tiemann, R.Depping, E.Gineikiene, L.Kaliniene, R.Nivinskas, and W.Rüger (2004).
ModA and ModB, two ADP-ribosyltransferases encoded by bacteriophage T4: catalytic properties and mutation analysis.
  J Bacteriol, 186, 7262-7272.  
15311272 J.Sun, A.W.Maresso, J.J.Kim, and J.T.Barbieri (2004).
How bacterial ADP-ribosylating toxins recognize substrates.
  Nat Struct Mol Biol, 11, 868-876.  
  12718740 A.E.Frankel, D.R.Fleming, B.L.Powell, and R.Gartenhaus (2003).
DAB389IL2 (ONTAK) fusion protein therapy of chronic lymphocytic leukaemia.
  Expert Opin Biol Ther, 3, 179-186.  
12721285 C.Bourgeois, I.Okazaki, E.Cavanaugh, M.Nightingale, and J.Moss (2003).
Identification of regulatory domains in ADP-ribosyltransferase-1 that determine transferase and NAD glycohydrolase activities.
  J Biol Chem, 278, 26351-26355.  
11814347 C.Wilde, I.Just, and K.Aktories (2002).
Structure-function analysis of the Rho-ADP-ribosylating exoenzyme C3stau2 from Staphylococcus aureus.
  Biochemistry, 41, 1539-1544.  
12029083 J.Ménétrey, G.Flatau, E.A.Stura, J.B.Charbonnier, F.Gas, J.M.Teulon, M.H.Le Du, P.Boquet, and A.Menez (2002).
NAD binding induces conformational changes in Rho ADP-ribosylating clostridium botulinum C3 exoenzyme.
  J Biol Chem, 277, 30950-30957.
PDB codes: 1gze 1gzf
11807091 N.G.Haigh, and A.E.Johnson (2002).
A new role for BiP: closing the aqueous translocon pore during protein integration into the ER membrane.
  J Cell Biol, 156, 261-270.  
11264460 H.C.Lee (2001).
Physiological functions of cyclic ADP-ribose and NAADP as calcium messengers.
  Annu Rev Pharmacol Toxicol, 41, 317-345.  
11134535 J.C.Tanny, and D.Moazed (2001).
Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: Evidence for acetyl transfer from substrate to an NAD breakdown product.
  Proc Natl Acad Sci U S A, 98, 415-420.  
11455601 K.A.Denessiouk, V.V.Rantanen, and M.S.Johnson (2001).
Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
  Proteins, 44, 282-291.  
11395467 M.G.Jobling, and R.K.Holmes (2001).
Biological and biochemical characterization of variant A subunits of cholera toxin constructed by site-directed mutagenesis.
  J Bacteriol, 183, 4024-4032.  
11114923 Y.Ma, and P.W.Ludden (2001).
Role of the dinitrogenase reductase arginine 101 residue in dinitrogenase reductase ADP-ribosyltransferase binding, NAD binding, and cleavage.
  J Bacteriol, 183, 250-256.  
10972829 H.Otto, D.Tezcan-Merdol, R.Girisch, F.Haag, M.Rhen, and F.Koch-Nolte (2000).
The spvB gene-product of the Salmonella enterica virulence plasmid is a mono(ADP-ribosyl)transferase.
  Mol Microbiol, 37, 1106-1115.  
10944393 H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.
  Proteins, 41, 47-57.  
10889035 K.M.Dolan, G.Lindenmayer, and J.C.Olson (2000).
Functional comparison of the NAD binding cleft of ADP-ribosylating toxins.
  Biochemistry, 39, 8266-8275.  
10735850 M.Nagahama, Y.Sakaguchi, K.Kobayashi, S.Ochi, and J.Sakurai (2000).
Characterization of the enzymatic component of Clostridium perfringens iota-toxin.
  J Bacteriol, 182, 2096-2103.  
10657208 R.K.Holmes (2000).
Biology and molecular epidemiology of diphtheria toxin and the tox gene.
  J Infect Dis, 181, S156-S167.  
10762264 S.K.Grunwald, M.J.Ryle, W.N.Lanzilotta, and P.W.Ludden (2000).
ADP-Ribosylation of variants of Azotobacter vinelandii dinitrogenase reductase by Rhodospirillum rubrum dinitrogenase reductase ADP-ribosyltransferase.
  J Bacteriol, 182, 2597-2603.  
10971585 Y.Matsushima-Hibiya, M.Watanabe, T.Kono, T.Kanazawa, K.Koyama, T.Sugimura, and K.Wakabayashi (2000).
Purification and cloning of pierisin-2, an apoptosis-inducing protein from the cabbage butterfly, Pieris brassicae.
  Eur J Biochem, 267, 5742-5750.  
10336461 B.K.Beattie, and A.R.Merrill (1999).
A fluorescence investigation of the active site of Pseudomonas aeruginosa exotoxin A.
  J Biol Chem, 274, 15646-15654.  
10521467 C.Munshi, D.J.Thiel, I.I.Mathews, R.Aarhus, T.F.Walseth, and H.C.Lee (1999).
Characterization of the active site of ADP-ribosyl cyclase.
  J Biol Chem, 274, 30770-30777.  
10494827 H.C.Lee (1999).
A unified mechanism of enzymatic synthesis of two calcium messengers: cyclic ADP-ribose and NAADP.
  Biol Chem, 380, 785-793.  
10448534 I.J.Okazaki, and J.Moss (1999).
Characterization of glycosylphosphatidylinositiol-anchored, secreted, and intracellular vertebrate mono-ADP-ribosyltransferases.
  Annu Rev Nutr, 19, 485-509.  
10485873 M.Watanabe, T.Kono, Y.Matsushima-Hibiya, T.Kanazawa, N.Nishisaka, T.Kishimoto, K.Koyama, T.Sugimura, and K.Wakabayashi (1999).
Molecular cloning of an apoptosis-inducing protein, pierisin, from cabbage butterfly: possible involvement of ADP-ribosylation in its activity.
  Proc Natl Acad Sci U S A, 96, 10608-10613.  
9521710 A.Ruf, G.de Murcia, and G.E.Schulz (1998).
Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling.
  Biochemistry, 37, 3893-3900.
PDB codes: 2paw 2pax 3pax 4pax
9529251 B.D.Hamman, L.M.Hendershot, and A.E.Johnson (1998).
BiP maintains the permeability barrier of the ER membrane by sealing the lumenal end of the translocon pore before and early in translocation.
  Cell, 92, 747-758.  
9792657 H.Barth, J.C.Preiss, F.Hofmann, and K.Aktories (1998).
Characterization of the catalytic site of the ADP-ribosyltransferase Clostridium botulinum C2 toxin by site-directed mutagenesis.
  J Biol Chem, 273, 29506-29511.  
9726960 I.J.Okazaki, and J.Moss (1998).
Glycosylphosphatidylinositol-anchored and secretory isoforms of mono-ADP-ribosyltransferases.
  J Biol Chem, 273, 23617-23620.  
10837618 I.Pastan, and R.J.Kreitman (1998).
Immunotoxins for targeted cancer therapy.
  Adv Drug Deliv Rev, 31, 53-88.  
9485425 J.Scheuring, P.J.Berti, and V.L.Schramm (1998).
Transition-state structure for the ADP-ribosylation of recombinant Gialpha1 subunits by pertussis toxin.
  Biochemistry, 37, 2748-2758.  
9572842 M.Degano, S.C.Almo, J.C.Sacchettini, and V.L.Schramm (1998).
Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor.
  Biochemistry, 37, 6277-6285.
PDB code: 2mas
9759501 V.L.Schramm (1998).
Enzymatic transition states and transition state analog design.
  Annu Rev Biochem, 67, 693-720.  
9160745 B.D.Hamman, J.C.Chen, E.E.Johnson, and A.E.Johnson (1997).
The aqueous pore through the translocon has a diameter of 40-60 A during cotranslational protein translocation at the ER membrane.
  Cell, 89, 535-544.  
9012663 C.E.Bell, and D.Eisenberg (1997).
Crystal structure of nucleotide-free diphtheria toxin.
  Biochemistry, 36, 481-488.
PDB code: 1sgk
  9336832 C.E.Bell, T.O.Yeates, and D.Eisenberg (1997).
Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes.
  Protein Sci, 6, 2084-2096.  
9208920 D.T.Crane, B.Bolgiano, and C.Jones (1997).
Comparison of the diphtheria mutant toxin, CRM197, with a Haemophilus influenzae type-b polysaccharide-CRM197 conjugate by optical spectroscopy.
  Eur J Biochem, 246, 320-327.  
  9416617 F.van den Akker, M.Pizza, R.Rappuoli, and W.G.Hol (1997).
Crystal structure of a non-toxic mutant of heat-labile enterotoxin, which is a potent mucosal adjuvant.
  Protein Sci, 6, 2650-2654.
PDB code: 1lt4
9148937 G.M.Culver, S.M.McCraith, S.A.Consaul, D.R.Stanford, and E.M.Phizicky (1997).
A 2'-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae.
  J Biol Chem, 272, 13203-13210.  
9659904 G.V.Louie, W.Yang, M.E.Bowman, and S.Choe (1997).
Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor.
  Mol Cell, 1, 67-78.
PDB code: 1xdt
9109661 J.Scheuring, and V.L.Schramm (1997).
Kinetic isotope effect characterization of the transition state for oxidized nicotinamide adenine dinucleotide hydrolysis by pertussis toxin.
  Biochemistry, 36, 4526-4534.  
9204866 J.Scheuring, and V.L.Schramm (1997).
Pertussis toxin: transition state analysis for ADP-ribosylation of G-protein peptide alphai3C20.
  Biochemistry, 36, 8215-8223.  
  19079637 P.J.Berti, S.R.Blanke, and V.L.Schramm (1997).
Transition State Structure for the Hydrolysis of NAD Catalyzed by Diphtheria Toxin.
  J Am Chem Soc, 119, 12079-12088.  
9315851 V.Rolli, M.O'Farrell, J.Ménissier-de Murcia, and G.de Murcia (1997).
Random mutagenesis of the poly(ADP-ribose) polymerase catalytic domain reveals amino acids involved in polymer branching.
  Biochemistry, 36, 12147-12154.  
8755499 A.Ruf, J.Mennissier de Murcia, G.de Murcia, and G.E.Schulz (1996).
Structure of the catalytic fragment of poly(AD-ribose) polymerase from chicken.
  Proc Natl Acad Sci U S A, 93, 7481-7485.
PDB codes: 1paw 1pax
8703907 B.K.Beattie, and A.R.Merrill (1996).
In vitro enzyme activation and folded stability of Pseudomonas aeruginosa exotoxin A and its C-terminal peptide.
  Biochemistry, 35, 9042-9051.  
8952460 B.K.Beattie, G.A.Prentice, and A.R.Merrill (1996).
Investigation into the catalytic role for the tryptophan residues within domain III of Pseudomonas aeruginosa exotoxin A.
  Biochemistry, 35, 15134-15142.  
8805549 F.van den Akker, S.Sarfaty, E.M.Twiddy, T.D.Connell, R.K.Holmes, and W.G.Hol (1996).
Crystal structure of a new heat-labile enterotoxin, LT-IIb.
  Structure, 4, 665-678.
PDB code: 1tii
8901875 G.S.Prasad, D.E.McRee, E.A.Stura, D.G.Levitt, H.C.Lee, and C.D.Stout (1996).
Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38.
  Nat Struct Biol, 3, 957-964.
PDB code: 1lbe
8798630 H.M.Muller-Steffner, A.Augustin, and F.Schuber (1996).
Mechanism of cyclization of pyridine nucleotides by bovine spleen NAD+ glycohydrolase.
  J Biol Chem, 271, 23967-23972.  
8692916 M.Li, F.Dyda, I.Benhar, I.Pastan, and D.R.Davies (1996).
Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation.
  Proc Natl Acad Sci U S A, 93, 6902-6906.
PDB code: 1aer
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.